Protein fragment complementation assays for the detection of biological or drug interactions

ABSTRACT

We describe a strategy for designing and implementing protein-fragment complementation assays (PCAs) to detect biomolecular interactions in vivo and in vitro. The design, implementation and broad applications of this strategy are illustrated with a large number of enzymes with particular detail provided for the example of murine dihydrofolate reductase (DHFR). Fusion peptides consisting of N- and C-terminal fragments of murine DHFR fused to GCN4 leucine zipper sequences were coexpressed in  Escherichia coli  grown in minimal medium, where the endogenous DHFR activity was inhibited with trimethoprim. Coexpression of the complementary fusion products restored colony formation. Survival only occurred when both DHFR fragments were present and contained leucine-zipper forming sequences, demonstrating that reconstitution of enzyme activity requires assistance of leucine zipper formation. DHFR fragment-interface point mutants of increasing severity (Ile to Val, Ala and Gly) resulted in a sequential increase in  E. coli  doubling times illustrating the successful DHFR fragment reassembly rather than non-specific interactions between fragments. This assay could be used to study equilibrium and kinetic aspects of molecular interactions including protein-protein, protein-DNA, protein-RNA, protein-carbohydrate and protein-small molecule interactions, for screening cDNA libraries for binding of a target protein with unknown proteins or libraries of small organic molecules for biological activity. The selection and design criteria applied here is developed for numerous examples of clonal selection, colorometric, fluorometric and other assays based on enzymes whose products can be measured. The development of such assay systems is shown to be simple, and provides for a diverse set of protein fragment complementation applications.

FIELD OF THE INVENTION

The present invention relates to the determination of the function ofnovel gene products. The invention further relates to Protein fragmentComplementation Assays (PCA). PCAs allow for the detection of a widevariety of types of protein-protein, protein-RNA, protein-DNA,Protein-carbohydrate or protein-small organic molecule interactions indifferent cellular contexts appropriate to the study of suchinteractions.

BACKGROUND OF THE INVENTION

Many processes in biology, including transcription, translation, andmetabolic or is signal transduction pathways, are mediated bynoN-covalently-associated multienzyme complexes^(1, 101). The formationof multiprotein or protein-nucleic acid complexes produce the mostefficient chemical machinery. Much of modern biological research isconcerned with identifying proteins involved in cellular processes,determining their functions and how, when, and where they interact withother proteins involved in specific pathways. Further, with rapidadvances in genome sequencing projects there is a need to developstrategies to define “protein linkage maps”, detailed inventories ofprotein interactions that make up functional assemblies ofproteins^(2,3). Despite the importance of understanding protein assemblyin biological processes, there are few convenient methods for studyingprotein-protein interactions in vivo^(4,5). Approaches include the useof chemical crosslinking reagents and resonance energy transfer betweendye-coupled proteins^(102, 103). A powerful and commonly used strategy,the yeast two-hybrid system, is used to identify novel protein-proteininteractions and to examine the amino acid determinants of specificprotein interactions^(4,6-8). The approach allows for rapid screening ofa large number of clones, including cDNA libraries. Limitations of thistechnique include the fact that the interaction must occur in a specificcontext (the nucleus of S. cerevisiae), and generally cannot be used todistinguish induced versus constitutive interactions.

Recently, a novel strategy for detecting protein-protein interactionshas been demonstrated by Johnsson and Varshaysky¹⁰⁸ called theubiquitin-based split protein sensor (USPS)⁹. The strategy is based oncleavage of proteins with N-terminal fusions to ubiquitin by cytosolicproteases (ubiquitinases) that recognize its tertiary structure. Thestrategy depends on the reassembly of the tertiary structure of theprotein ubiquitin from complementary N- and C-terminal fragments andcrucially, on the augmentation of this reassembly by oligomerizationdomains fused to these fragments. Reassembly is detected as specificproteolysis of the assembled product by cytosolic proteases(ubiquitinases). The authors demonstrated that a fusion of a reporterprotein-ubiquitin C-terminal fragment could also be cleaved byubiquitinases, but only if co-expressed with an N-terminal fragment ofubiquitin that was complementary to the C-terminal fragment. Thereconstitution of observable ubiquitinase activity only occurred if theN- and C-terminal fragments were bound through GCN4 leucinezippers^(109,110). The authors suggested that this “split-gene” strategycould be used as an in vivo assay of protein-protein interactions andanalysis of protein assembly kinetics in cells. Unfortunately, thisstrategy requires additional cellular factors (in this caseubiquitinases) and the detection method does not lend itself tohigh-throughput screening of cDNA libraries.

Rossi, F., C. A. Charlton, and H. M. Blau (1997) Proc. Nat. Acad. Sci.(USA) 94, 8405-8410) have reported an assay based on the classicalcomplementation of α and ω fragments of β-galactosidase (β-gal) andinduction of complementation by induced oligomerization of the proteinsFKBP12 and the mammalian target of rapamycin by rapamycin in transfectedC2C12 myoblast cell lines. Reconstitution of b-gal activity is detectedusing substrate fluorescein di-β-D-galactopyranoside using severalfluorescence detection assays. While this assay bears some resemblanceto the present invention, there are several significant distinguishingdifferences. First, this particular complementation approach has beenused for over thirty years in a vast number of applications includingthe detection of protein-protein interactions. Krevolin, M. and D. Kates(1993) U.S. Pat. No. 5,362,625) teaches the use of this complementationto detect protein-protein interactions. Also achievement of β-galcomplementation in mammalian cells has previously been reported(Moosmann, P. and S. Rusconi (1996) Nucl. Acids Res. 24, 1171-1172). Theindividual PCAs presented here are completely de novo designedinteraction detection assays, not described in any way previously exceptfor publications arising from applicants laboratory. Secondly, thisapplication describes a general strategy to develop molecularinteraction assays from a large number of enzyme or protein detectors,all de novo designed assays, whereas the β-gal assay is not novel, norare any general strategies or advancements over previously welldocumented applications given.

As in the USPS, the yeast-two hybrid strategy requires additionalcellular machinery for detection that exist only in specific cellularcompartments. There is therefore a need for a detection system whichuses the reconstitution of a specific enzyme activity from fragments asthe assay itself, without the requirement for other proteins for thedetection of the activity. Preferably, the assay would involve anoligomerization-assisted complementation of fragments of monomeric ormultimeric enzymes that require no other proteins for the detection oftheir activity. Furthermore, if the structure of an enzyme were known itwould be possible to design fragments of the enzyme to ensure that thereassembled fragments would be active and to introduce mutations toalter the stringency of detection of reassembly. However, knowledge ofstructure is not a prerequisite to the design of complementingfragments, as will be explained below. The flexibility allowed in thedesign of such an approach would make it applicable to situations whereother detection systems may not be suitable.

Recent advances in human genomics research has led to rapid progress inthe identification of novel genes. In applications to biological andpharmaceutical research, there is now the pressing need to determine thefunctions of novel gene products; for example, for genes shown to beinvolved in disease phenotypes. It is in addressing questions offunction where genomics-based pharmaceutical research becomes boggeddown and there is now the need for advances in the development of simpleand automatable functional assays. A first step in defining the functionof a novel gene is to determine its interactions with other geneproducts in an appropriate context; that is, since proteins makespecific interactions with other proteins or other biopolymers as partof functional assemblies, an appropriate way to examine the function ofa novel gene is to determine its physical relationships with theproducts of other genes.

Screening techniques for protein interactions, such as the yeast“two-hybrid” system, have transformed molecular biology, but can only beused to study specific types of constitutively interacting proteins orinteractions of proteins with other molecules, in narrowly definedcellular and compartmental contexts and require a complex cellularmachinery (transcription) to work. To rationally screen for proteininteractions within the context of a specific problem requires moreflexible approaches. Specifically, assays that meet criteria necessarynot only to detecting molecular interactions, but also to validatingthese interactions as specific and biologically relevant.

A list of assay characteristics that meet such criteria are as follows:

1) Allow for the detection of protein-protein, protein-DNA/RNA orprotein-drug interactions in vivo or in vitro.2) Allow for the detection of these interactions in appropriatecontexts, such as within a specific organism, cell type, cellularcompartment, or organelle.3) Allow for the detection of induced versus constitutiveprotein-protein interactions (such as by a cell growth or inhibitoryfactor).4) To be able to distinguish specific versus non-specificprotein-protein interactions by controlling the sensitivity of theassay.5) Allow for the detection of the kinetics of protein assembly in cells.6) Allow for screening of cDNA, small organic molecule, or DNA or RNAlibraries for molecular interactions.

SUMMARY OF THE INVENTION

The present invention seeks to provide the above-mentioned needs forwhich the prior art is silent. The present invention provides a generalstrategy for detecting protein interactions with other biopolymersincluding other proteins, nucleic acids, carbohydrates or for screeningsmall molecule libraries for compounds of potential therapeutic value.In a preferred embodiment, the instant invention seeks to provide anoligomerization-assisted complementation of fragments of monomericenzymes that require no other proteins for the detection of theiractivity. In one such embodiment, a protein-fragment complementationassay (PCA) based on reconstitution of dihydrofolate reductase activityby complementation of defined fragments of the enzyme in E. coli ishereby provided. This assay requires no additional endogenous factorsfor detecting specific protein-protein interactions (i.e. leucine zipperinteractions) and can be conveniently extended to screening cDNA,nucleic acid, small molecule or protein design libraries for molecularinteractions. In addition, the assay can also be adapted for detectionof protein interactions in any cellular context or compartment and beused to distinguish between induced versus constitutive proteininteractions in both prokaryotic and eukaryotic systems.

One particular strategy for designing a protein complementation assay(PCA) is based on using the following characteristics: 1) A protein orenzyme that is relatively small and monomeric, 2) for which there is alarge literature of structural and functional information, 3) for whichsimple assays exist for the reconstitution of the protein or activity ofthe enzyme, both in vivo and in vitro, and 4) for which overexpressionin eukaryotic and prokaryotic cells has been demonstrated. If thesecriteria are met, the structure of the enzyme is used to decide the bestposition in the polypeptide chain to split the gene in two, based on thefollowing criteria: 1) The fragments should result in subdomains ofcontinuous polypeptide; that is, the resulting fragments will notdisrupt the subdomain structure of the protein, 2) the catalytic andcofactor binding sites should all be contained in one fragment, and 3)resulting new N- and C-termini should be on the same face of the proteinto avoid the need for long peptide linkers and allow for studies oforientation-dependence of protein binding.

It should be understood that the above mentioned criteria do not allneed to be satisfied for a proper working of the present invention. Itis an advantage that the enzyme be small, preferably between 10-40 kDa.Although monomeric enzymes are preferred, multimeric enzymes can also beenvisaged as within the scope of the present invention. The dimericprotein tyrosinase can be used in the instant assay. The information onthe structure of the enzyme provides an additional advantage indesigning the PCA, but is not necessary. Indeed, an additional strategy,to develop PCAs is presented, based on a combination of exonucleasedigestion-generated protein fragments followed by directed proteinevolution in application to the enzyme aminoglycoside kinase. Althoughthe overexpression in prokaryotic cells is preferred it is not anecessity. It will be understood to the skilled artisan that the enzymecatalytic site (of the chosen enzyme) does not absolutely need to be onsame molecule.

The present application explains the rationale and criteria for using aparticular enzyme in a PCA. FIG. 1 shows a general description of a PCA.The gene for a protein or enzyme is rationally dissected into two ormore fragments. Using molecular biology techniques, the chosen fragmentsare subcloned, and to the 5′ ends of each, proteins that either areknown or thought to interact are fused. Co-transfection ortransformation these DNA constructs into cells is then carried out.Reassembly of the probe protein or enzyme from its fragments iscatalyzed by the binding of the test proteins to each other, andreconstitution is observed with some assay. It is crucial to understandthat these assays will only work if the fused, interacting proteinscatalyze the reassembly of the enzyme. That is, observation ofreconstituted enzyme activity must be a measure of the interaction ofthe fused proteins.

A preferred embodiment of the present invention focuses on a PCA basedon the enzyme dihydrofolate reductase. Expansion of the strategy toinclude assays in eukaryotic, cells, library screening, and a specificapplication to problems concerning the study of integrated biochemicalpathways such as signal transduction pathways, is presented. Additionalassays, including those based on enzymes that can act as dominant orrecessive drug selection or metabolic salvage pathways are disclosed. Inaddition, PCAs based on enzymes that will produce a colored orfluorescent product are also disclosed. The present invention teacheshow the PCA strategy can be both generalized and automated forfunctional testing of novel genes, screening of natural products orcompound libraries for pharmacological activity and identification ofnovel gene products that interact with DNA, RNA or carbohydrates aredisclosed. It also teaches how the PCA strategy can be applied toidentifying natural products or small molecules from compound librariesof potential therapeutic value that can inhibit or activate suchmolecular interactions and how enzyme substrates and small moleculeinhibitors of enzymes can be identified. Finally, it teaches how the PCAstrategy can be used to perform protein engineering experiments thatcould lead to designed enzymes with industrial applications or peptideswith biological activity.

Simple strategies to design and implement assays for detecting proteininteractions in vivo are disclosed herein. We have designedcomplementary fragments of the native mDHFR that, when coexpressed in E.coli grown in minimal medium, allow for survival of clones expressingthe two fragments, where the basal activity of the endogenous bacterialDHFR is inhibited by the competitive inhibitor trimethoprim (FIG. 3).Reconstitution of activity only occurred when both N- and C-terminalfragments of DHFR were coexpressed as C-terminal fusions to GCN4 leucinezipper sequences, indicating that reassembly of the fragments requiresformation of a leucine zipper between the N- and C-terminal fusionpeptides. The sequential increase in cell doubling times resulting fromthe destabilizing mutations directed at the assembly interface (Ile114to Val, Ala or Gly) demonstrates that the observed cell survival underselective conditions is a result of the specific,leucine-zipper-assisted association of mDHFR fragment[1,2] withfragment[3], as opposed to nonspecific interactions of Z-F[3] withZ-F[1,2]. several detailed and many additional examples are given.

As demonstrated previously with the ubiquitin-based split protein sensor(USPS)⁹, a protein-fragment complementation strategy can be used tostudy equilibrium and kinetic aspects of protein-protein interactions invivo. The DHFR and other PCAs however, are simpler assays. They arecomplete systems; no additional endogenous factors are necessary and theresults of complementation are observed directly, with no furthermanipulation. The E. coli cell survival assay described herein shouldtherefore be particularly useful for screening cDNA libraries forprotein-protein interactions. mDHFR expression in cells can be monitoredby binding of fluorescent high-affinity substrate analogues for DHFR²⁶.

There are several further aspects of the PCAs that distinguish them fromall other strategies for studying protein-protein interactions in vivo(except USPS). We have designed complementary fragments of enzymes thatallow for controlling the stringency of the assay, and could be used toobtain estimates of the kinetics and equilibrium constants forassociation of two proteins. For example, with DHFR the point mutationsof the wild-type enzyme Ile 114 to Val, Ala, or Gly alter the stringencyof reconstitution of DHFR activity. For determining estimates ofequilibrium and kinetic parameters for a specific protein-proteininteraction, one could perform a series of DHFR PCA experiments with twoproteins that interact with a known affinity, using the wild type ordestabilizing mutant DHFR fragments. Comparison of cell growth rates inthis model system with rates for a DHFR PCA using unknowns would give anestimate of the strength of the unknown interaction.

It should be understood that the present invention should not be limitedto the DHFR or other PCAs presented, as it is only non-limitingembodiments of the protein complementation assay of the presentinvention. Moreover, the PCAs should not be limited in the context inwhich they could be used. Constructs could be designed for targeting thePCA fusions to specific compartments in the cell by addition ofsignaling peptide sequences^(27,28). Induced versus constitutiveprotein-protein interactions could be distinguished by a eukaryoticversion of the PCA, in the case of an interaction that is triggered by abiochemical event. Also, the system could be adapted for use inscreening for novel, induced protein-molecular associations between atarget protein and an expression library.

The instant invention is also directed to a method for detectingbiomolecular interactions said method comprising:

(a) selecting an appropriate reporter molecule;

(b) effecting fragmentation of said reporter molecule such that saidfragmentation results in reversible loss of reporter function;

(c) fusing or attaching fragments of said reporter molecule separatelyto other molecules; followed by

(d) reassociation of said reporter fragments through interactions of themolecules that are fused to said fragments.

The invention also provides molecular fragment complementation assaysfor the detection of molecular interactions comprising a reassembly ofseparate fragments of a molecule, wherein reassembly of said fragmentsis operated by the interaction of molecular domains fused to eachfragment of said molecules, and wherein reassembly of the fragments isindependent of other molecular processes.

In another aspect, the present invention is directed to a method oftesting biomolecular interactions comprising:

a) generating a first fusion product comprising

-   -   i) a first fragment of a first molecule and    -   ii) a second molecule which is different or the same as said        first molecule;

b) generating a second fusion product comprising

-   -   i) a second fragment of said first molecule; and    -   ii) a third molecule which is different from or the same as said        first molecule or second molecule;

c) allowing the first and second fusion products to contact each other;and

d) testing for activity regained by association of the recombinedfragments of the first molecule, wherein said reassociation is mediatedby interaction of the second and third molecules.

In another novel feature, the invention is directed to a methodcomprising an assay where fragments of a first molecule are fused to asecond molecule and fragment association is detected by reconstitutionof the first molecule's activity.

The present invention also provides a composition comprising a productselected from the group consisting of:

(a) a first fusion product comprising:

-   -   1) a first fragment of a first molecule whose fragments can        exhibit a detectable activity when associated and

2) a second molecule that can bind (a)(1);

(b) a second fusion product comprising

-   -   1) a second fragment of said first molecule and    -   2) a third molecule that can bind (b)(1); and

c) both (a) and (b).

The invention further provides a composition comprising complementaryfragments of a first molecule, each fused to a separate fragment of asecond molecule.

The inventors of the present subject matter further provide acomposition comprising a nucleic acid molecule coding for a fusionproduct, which molecule comprises sequences coding for a productselected from the group consisting of:

(a) a first fusion product comprising:

-   -   1) fragments of a first molecule whose fragments can exhibit a        detectable activity when associated and    -   2) a second molecule fused to the fragment of the first        molecule;

(b) a second fusion product comprising

-   -   1) a second fragment of said first molecule and    -   2) a second or third molecule; and

(c) both (a) and (b).

The present invention is also directed to a method of testing forbiomolecular interactions associated with: (a) complementary fragmentsof a first molecule whose fragments can exhibit a detectable activitywhen associated or (b) binding of two protein-protein interactingdomains from a second or third molecule, said method comprising:

-   -   1) creating a fusion of        -   (a) a first fragment of a first molecule whose fragments can            exhibit a detectable activity when associated and        -   (b) a first protein-protein interacting domain;    -   2) creating a fusion of        -   (a) a second fragment of said first molecule and        -   (b) a second protein-protein interacting domain that can            bind said first protein-protein interacting domain;    -   3) allowing the fusions of (1) and (2) to contact each other;        and    -   4) testing for said activity.

The instant invention further provides a composition comprising aproduct selected from the group consisting of:

(a) a first fusion product comprising:

-   -   1) a first fragment of a molecule whose fragments can exhibit a        detectable activity when associated and    -   2) a first protein-protein interacting domain;

(b) a second fusion product comprising

-   -   1) a second fragment of said first molecule and    -   2) a second protein-protein interacting domain that can bind        said first protein-protein interacting domain; and

(c) both (a) and (b).

The invention is also directed to a composition comprising a nucleicacid molecule coding for a fusion product, which molecule comprisessequences coding for either:

(a) a first fusion product comprising:

-   -   1) a first fragment of a molecule whose fragments can exhibit a        detectable activity when associated and    -   2) a first protein-protein interacting domain; or

(b) a second fusion product comprising

-   -   1) a second fragment of said molecule and    -   2) a second protein-protein interacting domain that can bind        said first protein-protein interacting domain; or

(c) both (a) and (b).

The invention also provides a method of detecting kinetics of proteinassembly and screening cDNA libraries comprising performing PCA.

In another embodiment, the invention further provides a method oftesting the ability of a compound to inhibit molecular interactions in aPCA comprising performing a PCA in the presence of said compound andcorrelating any inhibition with said presence.

In a further embodiment, the invention provides a method for detectingprotein-protein interactions in living organisms and or cells, whichmethod comprises:

(a) synthesizing probe protein fragments from an enzyme which enablesdominant selection by dissecting the gene coding for the enzyme into atleast two fragments;

(b) constructing fusion proteins with one or more molecules that are tobe tested for interactions;

(c) fusing the proteins obtained in (b) with one or more of the probefragments;

(d) coexpressing the fusion proteins; and

(e) detecting the reconstitution of enzyme activity.

The invention still provides a method for detecting biomolecularinteractions said method comprising:

(a) selecting an appropriate reporter molecule;

(b) effecting fragmentation of said reporter molecule;

(c) fusing or attaching fragments of said reporter molecule separatelyto other molecules; followed by

(d) reassociation of said reporter fragments through interactions of themolecules that are fused to said fragments.

Lastly, the invention also provides a novel method of affecting genetherapy, which includes the step of providing the assays andcompositions described above.

The present invention is pioneering as it is the first proteincomplementation assay displaying such a level of simplicity andversatility. The exemplified embodiments are protein-fragmentcomplementation assays (PCA) based on mDHFR, where a leucine zipperdirects the reconstitution of DHFR activity. Activity was detected by anE. coli survival assay which is both practical and inexpensive. Thissystem illustrates the use of mDHFR fragment complementation in thedetection of leucine zipper dimerization and could be applied to thedetection of unknown, specific protein-molecular interactions in vivo.

It should be understood that the instant invention is not limited to thePCAs presented here, as numerous other enzymes can be selected and usedin accordance with the teachings of the present invention. Examples ofsuch markers can be found in Kaufman, (1987 Genetic Eng. 9:155-198) andreferences found therein as well as table 1 of this application.

It should also be clear to the skilled artisan to which the presentinvention pertains that the invention is not limited to the use ofleucine zippers as the two interacting molecules. Indeed, numerous othertypes of protein-molecule interactions can be used and identified inaccordance with the teaching of the present invention. The known typesof motifs involved in protein-molecular interactions are well known inthe art.

The present application refers to numerous prior art documents and theentire contents of all those prior art documents are herein incorporatedby reference.

Other features and advantages of the present invention will be apparentfrom the following description of the preferred embodiments thereof, theappended Examples and from the enjoined claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides a general description of a PCA. Using molecular biologytechniques, the chosen fragments of the enzyme are subcloned, and to the5′ ends of each, proteins that either are known or thought to interactare fused. Co-transfection or transformation these DNA constructs intocells is then carried out and reconstitution with some assay isobserved.

FIG. 2 is a scheme of the fusion constructs used in one of theembodiments of the invention. The hexahistidine peptide (6His), thehomodimerizing GCN4 leucine zipper (Zipper) and mDHFR fragments (1, 2and 3) are illustrated. The labels for the constructs are used toidentify both the DNA constructs and the proteins expressed from theseconstructs.

FIG. 3: (A) shows E. coli survival assay on minimal medium plates.Control: Left side of the plate: E. coli harboring pQE-30 (no insert);right side: E. coli harboring pQE-16, coding for native mDHFR. Panel I:Left side of each plate: transformation with construct Z-F[1,2]; rightside of each plate: transformation with construct Z-F[3]. Panel II:Cotransformation with constructs Z-F[1,2] and Z-F[3]. Panel III:Cotransformation with constructs Control-F[1,2] and Z-F[3]. All platescontain 0.5 mg/ml trimethoprim. In panels I to III, plates on the rightside contain 1 mM IPTG.

(B) E. coli survival assay using destabilizing DHFR mutants. Panel I:Cotransformation of E. coli with constructs Z-F[1,2] andZ-F[3:Ile114Val]. Panel II: Cotransformation with Z-F[1,2] andZ-F[3:Ile114Ala]. Inset is a 5-fold enlargement of the right-side plate.Panel III: Cotransformation with Z-F[1,2] and Z-F[3:Ile114Gly]. Allplates contain 0.5 mg/ml trimethoprim. Plates on the right side contain1 mM IPTG.

FIG. 4 features the coexpression of mDHFR fragments. (A) Agarose gelanalysis of restriction pattern resulting from HincII digestion ofplasmid DNA. Lane 1 contains DNA isolated from E. coli cotransformedwith constructs Z-F[1,2] and Z-F[3]. Lanes 2 and 3 contain DNA isolatedfrom E. coli transformed with, respectively, construct Z-F[3] andconstruct Z-F[1,2]. Fragment migration (in bp) is indicated to theright.

(B) SDS-PAGE analysis of mDHFR fragment expression. Lanes 1 to 5 showcrude lysate of untransformed E. coli (lane 1), or E. coli expressingZ-F[1,2] (20.8 kDa; lane 2), Z-F[3] (18.4 kDa; lane 3), Control-F[1,2](14.2 kDa; lane 4), and Z-F[1,2]+Z-F[3] (lane 5). Lane 6 shows 40 ml outof 2 ml copurified Z-F[1,2] and Z-F[3]. Arrowheads point to the proteinsof interest. Migration of molecular weight markers (in kDa) is indicatedto the right.

FIG. 5 illustrates the general features of a PCA based on a survivalassay such as the DHFR PCA. The assay can be used in a bacterial or amammalian context. The inserted target DNA can be a known sequencecoding for a protein (or protein domain) of interest, or can be a cDNAlibrary.

FIG. 6 represents an autoradiograph of a COS cell lysate after a 30 min.³⁵S-Met-Cys pulse-labelling. The expression pattern is essentiallyidentical to that observed in E. coli (see FIG. 4). The DNA transfectedinto the cells (or cotransfected) is indicated above the respectivelanes.

FIG. 7 illustrates the results of a protein engineering application ofthe mDHFR bacterial PCA. Two semi-random leucine zipper libraries werecreated (as described in the text) and each inserted N-terminal to oneof the mDHFR fragments. Cotransformation of the resulting zipper-DHFRfragment libraries in E. coli and plating on selective medium allowedfor survival of clones harboring successfully interacting leucinezippers. Fourteen clones were isolated and the zippers were sequenced toidentify the residues at the “e” and “g” positions. The “e-g” pairs werecategorized, as having attractive pairing (charge:charge, charge:neutralpolar or neutral polar:neutral polar) or repulsive pairing(charge:charge) and the number of each type of interaction scored foreach clone. The total number of interactions for each clone is 6; theinteractions are tallied on the histogram.

Other objects, advantages and features of the present invention willbecome more apparent upon reading of the following non-restrictivedescription of preferred embodiments with reference to the accompanyingdrawings which are exemplary and should not be interpreted as limitingthe scope of the present invention.

DESCRIPTION OF THE PREFERRED EMBODIMENTS

Selection of mDHFR for a PCA.

In designing a protein-fragment complementation assay (PCA), we soughtto identify an enzyme for which the following is true: 1) An enzyme thatis relatively small and monomeric, 2) for which structural andfunctional information exists, 3) for which simple assays exist for bothin vivo and in vitro measurement, and 4) for which overexpression ineukaryotic and prokaryotic cells has been demonstrated. Murine DHFR(mDHFR) meets all of the criteria for a PCA listed above. Prokaryoticand eukaryotic DHFR is central to cellular one-carbon metabolism and isabsolutely required for cell survival in both prokaryotes andeukaryotes. Specifically it catalyses the reduction of dihydrofolate totetrahydrofolate for use in transfer of one-carbon units required forbiosynthesis of serine, methionine, purines and thymidylate. The DHFRsare small (17 kD to 21 kD), monomeric proteins. The crystal structuresof DHFR from various bacterial and eukaryotic sources are known andsubstrate binding sites and active site residues have beendetermined¹¹¹⁻¹¹⁴, allowing for rational design of protein fragments.The folding, catalysis, and kinetics of a number of DHFRs have beenstudied extensively¹¹⁵⁻¹¹⁹. The enzyme activity can be monitored invitro by a simple spectrophotometric assay¹²⁰, or in vivo by cellsurvival in cells grown in the absence of DHFR end products. DHFR isspecifically inhibited by the anti-folate drug trimethoprim. Asmammalian DHFR has a 12000-fold lower affinity for trimethoprim thandoes bacterial DHFR¹²¹, growth of bacteria expressing mDHFR in thepresence of trimethoprim levels lethal to bacteria is an efficient meansof selecting for reassembly of mDHFR fragments into active enzyme. Highlevel expression of mDHFR has been demonstrated in transformedprokaryote or transfected eukaryotic cells¹²²⁻¹²⁶.

Design Considerations.

mDHFR shares high sequence identity with the human DHFR (hDHFR) sequence(91% identity) and is highly homologous to the E. coli enzyme (29%identity, 68% homology) and these sequences share visuallysuperimposable tertiary structure¹¹¹. Comparison of the crystalstructures of mDHFR and hDHFR suggests that their active sites areessentially identical^(127,128). DHFR has been described as being formedof three structural fragments forming two domains^(129, 130) the adeninebinding domain (residues 47 to 105=fragment[2]) and a discontinuousdomain (residues 1 to 46=fragment[1] and 106 to 186 [3]; numberingaccording to the murine sequence). The folate binding pocket and theNADPH binding groove are formed mainly by residues belonging tofragments[1] and [2]. Fragment [3] is not directly implicated incatalysis.

Residues 101 to 108 of hDHFR, at the junction between fragment[2] andfragment[3], form a disordered loop which lies on the same face of theprotein as both termini. We chose to cleave mDHFR between fragments[1,2] and [3], at residue 107, so as to cause minimal disruption of theactive site and NADPH cofactor binding sites. The native N-terminus ofmDHFR and the novel N-terminus created by cleavage occur on the samesurface of the enzyme^(112, 128) allowing for ease of N-terminalcovalent attachment of each fragment to associating fragments such asthe leucine zippers used in this study. Using this system, we haveobtained leucine-zipper assisted assembly of the mDHFR fragments intoactive enzyme.

Example 1 Experimental Protocol DNA Constructs.

Mutagenic and sequencing oligonucleotides were purchased from Gibco BRL.Restriction endonucleases and DNA modifying enzymes were from Pharmaciaand New England Biolabs. The mDHFR fragments carrying their own iN-framestop codon were subcloned into pQE-32 (Qiagen), downstream from andiN-frame with the hexahistidine peptide and a GCN4 leucine zipper (FIG.1; FIG. 2). All final constructs were based on the Qiagen pQE series ofvectors, which contain an inducible promoter-operator element (tac), aconsensus ribosomal binding site, initiator codon and nucleotides codingfor a hexahistidine peptide. Full-length mDHFR is expressed from pQE-16(Qiagen).

Expression Vector Harboring the GCN4 Leucine Zipper

Residues 235 to 281 of the GCN4 leucine zipper (a SalI/BamHI 254 bpfragment) were obtained from a yeast expression plasmid pRS316⁹. Therecessed terminus at the BamHI site was filled-in with Klenow polymeraseand the fragment was ligated to pQE-32 linearized withSalI/HindIII(filled-in). The product, construct Z, carries an openreading frame coding for the sequence Met-Arg-Gly-Ser followed by ahexahistidine tag and 13 residues preceding the GCN4 leucine zipperresidues.

Creation of DHFR Fragments:

The eukaryotic transient expression vector, pMT3 (derived from pMT2)¹⁶,was used as a template for PCR-generation of mDHFR containing thefeatures allowing subcloning and separate expression of fragment[1,2]and fragment[3]. The megaprimer method of PCR mutagenesis²⁹ was used togenerate a full-length 590 bp product. Oligonucleotides complementary tothe nucleotide sequence coding for the N- and C-termini of mDHFR andcontaining a novel BspEI site outside the coding sequence were used aswell as an oligonucleotide used to create a novel stop codon afterfragment[1,2], followed by a novel SpeI site for use in subcloningfragment[3].

Construction of a New Multiple Cloning Region and Subcloning of DHFRFragments [1,2] and [3]

Complementary oligonucleotides containing the novel restriction sites:SnaBI, NheI, SpeI and BspEI, were hybridized together resulting in 5′and 3′ overhangs complementary to EcoRI, and inserted into pMT3 at aunique EcoRI site. The 590 bp PCR product (described above) was digestedwith BspEI and inserted into pMT3 linearized at BspEI, yieldingconstruct [1,2,3]. The 610 bp BspEI/EcoNI fragment (coding for DHFRfragment[1,2], followed by a novel stop and fragment[3] up to EcoNI) wasfilled in at EcoNI and subcloned into pMT3 opened with BspEI/HpaI,yielding construct F[1,2]. The 250 bp SpeI/BspEI fragment of construct[1,2,3] coding for DHFR fragment[3] (with no in-frame stop codon) wassubcloned into pMT3 opened with the same enzymes. The stop codon of thewild-type DHFR sequence, downstream from fragment[3] in pMT3, wasinserted as follows. Cleavage with EcoNI, present in both the insertedfragment[3] and the wild-type fragment[3], removal of the 683 bpintervening sequence and relegation of the vector yielded a construct offragment[3] with the wild-type stop codon, construct F[3].

Creation of the Expression Constructs

The 1051 bp and the 958 bp SnaBI/XbaI fragments of constructs F[1,2] andF[3], respectively, were subcloned into construct Z opened withBglII(filled-in)/NheI, yielding constructs Z-F[1,2] and Z-F[3] (FIG. 2).For the Control expression construct, the 180 bp XmaI/BspEI fragmentcoding for the zipper was removed from construct Z-F[1,2], yieldingconstruct Control-F[1,2] (FIG. 2).

Creation of Stability Mutants

Site-directed mutagenesis was performed³⁰ to produce mutants at Ile114(numbering of the wild-type mDHFR). The mutagenesis reaction was carriedout on the KpnI/BamHI fragment of construct Z-F[3] subcloned intopBluescript SK+ (Stratagene), using oligonucleotides that encode asilent mutation producing a novel BamHI site. The 206 bp NheI/EcoNIfragment of putative mutants identified by restriction was subclonedback into Z-F[3]. The mutations were confirmed by DNA sequencing.

E. coli Survival Assay

E. coli strain BL21 carrying plasmid pRep4 (from Qiagen, forconstitutive expression of the lac repressor) were made competent,transformed with the appropriate DNA constructs and washed twice withminimal medium before plating on minimal medium plates containing 50mg/ml kanamycin, 100 mg/ml ampicillin and 0.5 mg/ml trimethoprim. Onehalf of each transformation mixture was plated in the absence, and thesecond half in the presence, of 1 mM IPTG. All plates were placed at 37°C. for 66 hrs.

E. coli Growth Curves

Colonies obtained from cotransformation were propagated and used toinoculate 10 ml of minimal medium supplemented with ampicillin,kanamycin as well as IPTG (1 mM) and trimethoprim (1 μg/μl) whereindicated. Cotransformants of Z-F[1,2]+Z-F[3:Ile114Gly] were obtainedunder non-selective conditions by plating the transformation mixture onL-agar (+kanamycin and ampicillin) and screening for the presence of thetwo constructs by restriction analysis. All growth curves were performedin triplicate. Aliquots were withdrawn periodically for measurement ofoptical density. Doubling time was calculated for early logarithmicgrowth (OD 600 between 0.02 and 0.2).

Protein Overexpression and Purification

Bacteria were propagated in Terrific Broth³¹ in the presence of theappropriate antibiotics to an OD600 of approximately 1.0. Expression wasinduced by addition of 1 mM IPTG and further incubation for 3 hrs. Foranalysis of crude extract, pellets from 150 ml of induced cells werelysed by boiling in loading dye. The lysates were clarified bymicrocentrifugation and analyzed by SDS-PAGE32. For proteinpurification, a cell pellet from 50 ml of induced E. coli cotransformedwith constructs Z-F[1,2] and Z-F[3] was lysed by sonication, and adenaturing purification of the insoluble pellet undertaken using Ni-NTA(Qiagen) as described by the manufacturer. The proteins were eluted witha stepwise imidazole gradient. The fractions were analyzed by SDS-PAGE.

Results

Design of mDHFR Fragments for a PCA

mDHFR shares high sequence identity with the human DHFR (hDHFR)sequence. As the coordinates of the murine crystal structure were notavailable, we based our design considerations on the hDHFR structure.DHFR has been described as comprising three structural fragments formingtwo domains: the adenine binding domain (F[2]) and a discontinuousdomain (F[1] and F[3])^(13,18). The folate binding pocket and the NADPHbinding groove are formed mainly by residues belonging to F[1] and F[2].Residues 101 to 108 of hDHFR form a disordered loop which lies on thesame face of the protein as both termini. This loop occurs at thejunction between F[2] and F[3]. By cleaving mDHFR at residue 107, wecreated F[1,2] and F[3], thus causing minimal disruption of the activesite and substrate binding sites. The native N-terminus of mDHFR and thenovel N-terminus created by cleavage were covalently attached to theC-termini of GCN4 leucine zippers (FIG. 1).

E. coli Survival Assays

FIG. 2 illustrates the general features of the expressed constructs andthe nomenclature used in this study. FIG. 3 (panel A) illustrates theresults of cotransformation of bacteria with constructs coding forZ-F[1,2] and Z-F[3], in the presence of trimethoprim, clearly showingthat colony growth under selective pressure is possible only in cellsexpressing both fragments of mDHFR. There is no growth in the presenceof either Z-F[1,2] or Z-F[3] alone. Induction of protein expression withIPTG is essential for colony growth (FIG. 3A). The presence of theleucine zipper on both fragments of mDHFR is essential as illustrated bycotransformation of bacteria with both vectors coding for mDHFRfragments, only one of which carries a leucine zipper (FIG. 3A). Itshould be noted that growth of control E. coli transformed with thefull-length mDHFR is possible in the absence of IPTG due to low levelsof expression in uninduced cells.

Confirmation of the presence of both plasmids in bacteria able to growwith trimethoprim was obtained from restriction analysis of the plasmidDNA purified from isolated colonies. FIG. 4 (A) reveals the presence ofthe 1200 bp HincII restriction fragment from construct Z-F[1,2] as wellas the 487 and 599 bp HincII restriction fragments from constructZ-F[3]. Also present is the 935 bp HincII fragment of pRep4.Overexpression of the fusion proteins is illustrated in FIG. 4 (B). Inall cases, overexpression of a protein of the expected molecular weightis apparent on SDS-PAGE of the crude lysate. Purification of thecoexpressed proteins under denaturing conditions yielded two bands ofapparent homogeneity upon analysis by Coomassie-stained SDS-PAGE (FIG.4B).

Stability Mutants

Applicants generated mutants of F[3] to test whether reconstitution ofmDHFR activity by fragment assembly was specific. Protein stability canbe reduced by changing the side-chain volume in the hydrophobic core ofa protein^(9, 22-25). Residue Ile114 of mDHFR occurs in a core β-strandat the interface between F[1,2] and F[3], isolated from the active site.Ile 114 is in van der Waals contact with Ile51 and Leu93 in F[1,2]¹¹. Wemutated Ile 114 to Val, Ala, or Gly. FIG. 3 (panel B) illustrates theresults of cotransformation of E. coli with construct Z-F[1,2] and themutated Z-F[3] constructs. The colonies obtained from cotransformationwith Z-F[3:Ile114Ala] grew more slowly than those cotransformed withZ-F[3] or Z-F[3:Ile114Val] (see inset to FIG. 3B). No colony growth wasdetected in cells cotransformed with Z-F[3:Ile114Gly]. The number oftransformants obtained was not significantly different in the case wherecolonies were observed, implying that cells cotransformed with Z-F[1,2]and either Z-F[3], Z-F[3:Ile114Val] or Z-F[3:Ile114Ala] have an equalsurvival rate. Overexpression of the mutants Z-F[3:Ile114X] was in thesame range as Z-F[3], as determined by Coomassie-stained SDS-PAGE (datanot shown).

We also compared the relative efficiency of reassembly of mDHFRfragments by measuring the doubling time of the cotransformants inliquid medium. Doubling time in minimal medium was constant for alltransformants (data not shown). Selective pressure by trimethoprim inthe absence of IPTG prevented growth of E. coli except when transformedwith pQE-16 coding for full-length DHFR due to low levels of expressionin uninduced cells. Induction of mDHFR fragment expression with IPTGallowed survival of cotransformed cells (except in the case ofZ-F[1,2]+Z-F[3:Ile114Gly], although the doubling times weresignificantly increased relative to growth in the absence oftrimethoprim. The doubling time measured for cells expressingZ-F[1,2]+Z-F[3], Z-F[1,2]+Z-F[3:Ile114Val] and Z-F[1,2]+Z-F[3:Ile114Ala]were 1.6-fold, 1.9-fold and 4.1-fold, higher respectively, than thedoubling time of E. coli expressing pQE-16 in the absence oftrimethoprim and IPTG. The presence of IPTG unexpectedly preventedgrowth of E. coli transformed with full-length mDHFR. Growth waspartially restored by addition of the folate metabolism end-productsthymine, adenine, pantothenate, glycine and methionine (data not shown).This suggests that induced overexpression of mDHFR was lethal to E. coliwhen grown in minimal medium as a result of depletion of the folate poolby binding to the enzyme.

In another embodiment, applicants make point mutations in the GCN4leucine zipper of Z-F[1,2] and Z-F[3], for which direct equilibrium andkinetic parameters are known and correlating these known values withparameters derived from the PCA (Pelletier and Michnick, inpreparation). Comparison of cell growth rates in this model system withrates for a DHFR PCA using unknowns would give an estimate of thestrength of the unknown interaction. This should enable thedetermination of estimates of equilibrium and kinetic parameters for aspecific protein-protein interaction.

The present invention has illustrated and demonstrated aprotein-fragment complementation assay (PCA) based on mDHFR, where aleucine zipper directs the reconstitution of DHFR activity. Activity wasdetected by an E. coli survival assay which is both practical andinexpensive. This system illustrates the use of mDHFR fragmentcomplementation in the detection of leucine zipper dimerization andcould be applied to the detection of unknown, specific protein-proteininteractions in vivo.

E. coli Aminoglycoside Kinase: Optimization and Design of a PCA Using anExonuclease-Molecular Evolution Strategy

Although applicants have demonstrated that the engineering/designstrategy described above can be used to produce complementary enzymefragments, it is obvious that proteins did not evolve in such a way thatsuch fragments would be expected to have optimal physicalcharacteristics, including solubility, foldability (fast folding),protease resistance, or enzymatic activity. An alternative embodiment tothe engineering/design strategy is the endonuclease/evolution approach.This strategy can be used by itself or in conjunction with theengineering/design strategy. The advantages of this approach are that inprinciple, prior knowledge of the protein structure is not necessary,that the optimal fragments are chosen for PCA and that these fragmentswill also have optimal characteristics. Following selection of optimalcomplementary fragments, the fragments are exposed to multiple rounds ofrandom mutagenesis. Mutagenesis is achieved by suboptimal PCR combinedwith chemical mutagenesis or DNA shuffling (Stemmer, W. P. C. (1994)Proc, Natl, Acad, Sci. USA 91, 10747-10751). The overall strategy isdescribed for the case of aminoglycoside kinase (AK), an example ofantibiotic resistance marker that can be used for dominant selection ofprokaryotic cells such as E. coli or eukaryotic cells such as yeast ormammalian cell lines. The structure of an AK is already known, and sostrategy (1) would be possible, however we chose to combine bothstrategy (1) as defined for DHFR above, in conjunction with strategy(2).

Experimental Protocol

The optimization/selection procedure is as follows:

Generation of Library of AK Fragments Based on Products of ExonucleaseDigestion

Nested sets of deletions are created at the 5′ and the 3′ ends of the AKgene. In order to create unidirectional deletions, unique restrictionsites are introduced in the regions flanking the AK gene. At the 5′ and3′ termini, an “outer” sticky site with a protruding 3′ terminus (Sph Iand Kpn I, respectively) and an “inner” sticky site with recessed 3′terminus (Bgl II and Sal I, respectively) are added by PCR. Cleavage atSph I and Bgl II (or Kpn I and Sal I) results in creation of aprotruding terminus leading back to the flanking sequence and a recessedterminus leading into the AK gene. Digestion with E. coli exonucleaseIII and S1 nuclease (Henikoff, S. (1987) Methods in Enzymology 155,156-165) yields a set of nested deletions from the recessed terminusonly. Thus, 10 mg of DNA is digested with Sph I and Bgl II (or Kpn I andSal I), phenol-chloroform extracted, and 12.5 U exonuclease III added.At 30 sec intervals over 10 min, aliquots are taken and put intosolution with 2 U S1 nuclease. The newly created ends are filled in withT4 DNA polymerase (0.1 Upper sample) and the set of vectors closed backby blunt-ended ligation (10 U ligase per sample). The average length ofthe deletion at each time point is determined by restriction analysis ofthe sets. This yields sets of AK genes deleted from the 5′ or the 3′termini. This manipulation is undertaken directly in the pQE-32-Zipperconstructs, such that the products can be used directly in activityscreening.

Screening for AK Activity

As a first step in determining the requirements for fragmentcomplementation, we must determine the minimum N-terminal and C-terminalfragments of AK that, alone, are active. Sets of deletions areindividually transformed into E. coli BL21 cells and expression of theAK fragments is induced by IPTG. The sets where a significant number ofcolonies appear in the presence of G418 serve to indicate theapproximate length of N- and C-terminal AK fragments which retainactivity. Fragment complementation must therefore be undertaken withfragments taken from within these limits. The zipper-directed fragmentcomplementation is detected as follows: appropriate sets of deletions,or pools of sets, are cotransformed into BL21, expression is inducedwith IPTG and growth in the presence of varying G418 concentrations ismonitored. Large colonies which grow in the presence of high G418concentrations are selected as giving the most efficiently complementingproducts.

Directed evolution of optimal AK fragments using “DNA shuffling Afteroptimal fragments have been selected, the individual fragments areremoved by restriction digestion at Sph I and Kpn I allowing for 5′ and3′ constant priming regions flanking the N- or C-terminal complementaryfragments of AK. These oligonucleotides (2-4 μg) are digested withDNaseI (0.005 units/ul, 100 ul) and fragments of 10-50 nucleotides areextracted from low melting point agarose. PCR is then performed with thefragmented DNA, using Taq polymerase (2.5 units/up in a PCR mixturecontaining 0.2 mM dNTPs, 2.2 mM Mg2Cl (or 0 mM for subuptimal PCR), 50mM KCl, 10 mM Tris.HCl, pH 9.0, 0.1% TritonX-100. A PCR program of 94C/60 sec.; 94 C 30 sec.; 55 C 30 sec.; 72 C 30 sec. times 30 to 50; 72 C5 min. Samples are taken every 5 cycles after 25 cycles to monitor theappearance of reassembled complete fragments on agarose gel. Theprimerless PCR product is then diluted 1:40 or 1:60 and used as templatefor PCR with 5′, 3′ complementary constant region oligos as primers fora further 20 cycles. Final product is restriction digested with Sph Iand Kpn I and the products subcloned back into pQE32-Zipper to yield thefinal library of expression plasmids. As before, E. coli BL21 cells aresequentially transformed with C-terminal or N-terminal complementaryfragment-expression vectors at an estimated efficiency of 109 andfinally cells cotransformed with the complementary fragment. E. coli aregrown on agarose plates containing 1 μg/ml G418 and after 16 hours thelargest colonies are selected and grown in liquid medium at increasingconcentrations of G418. Those clones showing the maximal resistance toG418 are then selected and if maximum resistance or greater is reachedthe evolution is terminated. Otherwise the DNA shuffling procedure isrepeated. Finally, optimal fragments are sequenced and physicalproperties and enzymatic activity are assessed. This optimized AK PCA isnow ready to test for dominant selection in any other cell typeincluding yeast and mammalian cell lines. This strategy can be used todevelop any PCA based on enzymes that impart dominant or recessiveselection to a drug or toxin or to enzymes that produce a colored orfluorescent product. In the later two cases the end point of theevolution process is at minimum, reatainment of signal for the intact,wild type enzyme or enhancement of the signal. This strategy can also beused in the absence of knowledge of the enzyme structure, whether theenzyme in mono-, di- or multimeric structure. However, knowledge of theenzyme structure does not preclude applying this strategy as well, asdescribed below.

As can be appreciated, knowledge of the enzyme structure can be used torender a more efficient way of using molecular evolution to design aPCA. In this case, the enzyme structure is used to define minimaldomains of the protein in question, as was done for DHFR. Instead ofgenerating fragments of completely random length for the N- orC-terminal fragments, we select, during the exonuclease phase, thosefragments that at a minimum will code for one of the two domains. Forinstance, in the case of AK, two well defined domains can be discernedin the structure consisting of residues 1-94 in the N-terminus andresidues 95-267 in the C-terminus. Endonuclease digestions are performedas above, but reaction products are selected that will minimally codefor one of the two domains. These are then the starting points forfragment selection and evolution cycles as described above.

Heteromeric Enzyme PCA

A further embodiment of the invention relates to PCA based on usingheterodimeric or heteromultimeric enzymes in which the entire catalyticmachinery is contained within one independently folding subunit and theother subunit provides stability and/or a cofactor to the enzymaticsubunit. In this embodiment of PCA, the regulatory subunit is split intocomplementary fragments and fused to interacting proteins. Thesefragments are co-transformed/transfected into cells along with theenzyme subunit. As with single enzyme PCA described for DHFR and AK,reconstitution and detection of enzyme activity is dependent onoligomerization domaiN-assisted reassembly of the regulatory subunitreassembly into its native topology. However, the reconstituted subunitthen interacts with the intact enzymatic subunit to produce activity.This approach is reminiscent of the USPS system, except it has theadvantage that the enzyme in this case is not a constitutive cellularenzyme, but rather an exogenous gene product. As such there is noproblem with background activity from the host cell, the enzyme can beexpressed at higher levels than a natural gene and can also be modifiedto be directed to specific subcellular compartments (by subcloningcompartment-specific signal peptides onto the N- or C-termini of theenzyme and subunit fragments). The specific advantage of this approachis that while the single enzyme strategy may lead to suboptimalenzymatic activity, in this approach, the enzyme folds independently andmay in fact act as a chaperone to the fragmented regulatory subunit,aiding in its refolding. In addition, folding of the fragments may neednot be complete in order to impart regulation of the enzyme. Thisapproach is realized by a colorimetric/fluorometric assay we havedeveloped based on the Streptomyces tyrosinase. This enzyme catalyzesthe conversion of tyrosine to deoxyphenylalanine (DOPA). The reactioncan be measured by conversion of fluorocinyl-tyrosine to the DOPA form.The active enzyme consists of two subunits, the catalytic domain (Melc2)and a copper binding domain (Melc1). Meld is a small protein of 14 kDthat is absolutely required for Melc2 activity. In the assay we aredeveloping, the Meld protein is split into two fragments that serve asthe complementation part of the PCA. These fragments, fused tooligomerization domains, are coexpressed with Melc2, and the basis ofthe assay is that Melc2 activity is dependent on complementation of theMeld fragments. Stoichiometries of protein complexes can also beaddressed (i.e. whether a complex consists of two or three proteins) asfollows. One fuses two proteins to the two Melc1 fragments and a thirdto intact Melc2. It thus can be shown that the minimum complementaryactive complex of the tyrosinase will require that all three componentsand therefore a trimer is necessary. A key aspect of this approach isthat we can easily demonstrate specific interactions by making onecomponent, specifically the protein-Melc2 fusions catalytic subunitdependent on the other components by underexpressing it in thebackground of overexpressed Melc1 fragment-protein fusions.

Multimer Disruption-Based PCA

Although applicants have described only fragment complementation ofintact proteins, protein domains or subunits as comprising PCA, analternate embodiments relates to PCAs based on the disruption of theinterface between, for instance a dimeric enzyme that requires stableassociation of the subunits for catalytic activity. In such cases,selective or random mutagenesis at the subunit interface would disruptthe interaction and the basis of the assay would be that oligomerizationdomains fused to the subunits would provide the necessary binding energyto bring the subunits together into a functional enzyme.

Vector Design in Application to PCAs

The PCA strategies listed thus far have used two-plasmid transformationstrategies for expression of complementary fragments. This approach hassome advantages, such as using different drug resistance markers toselect for optimal incorporation of genes, for instance in transformedor transfected cells or for optimum transformation of complementaryplasmids into bacteria and control of expression levels of PCA fragmentsusing different promoters. However, single plasmid strategies haveadvantages in terms of simplicity of transfection/transformation.Protein expression levels can be controlled in different ways, whiledrug selection can be achieved in one of two ways: In the case of PCAsbased on survival assay using enzymes that are drug resistance markersthemselves, such as AK, or where the enzyme complements a metabolicpathway, such as DHFR, no additional drug resistance genes need beincorporated in the expression plasmids. If however the PCA is based onan enzyme that produces a colored or fluorescent product, such astyrosinase or firefly luciferase, an additional drug resistance genemust be expressed from the plasmid. Expression of PCA complementaryfragments and fused cDNA libraries/target genes can be assembled onsingle plasmids as individual operons under the control of separateinducible or constitutive promoters, or can be expressedpolycistronically. In E. coli polycistronic expression can be achievedusing known intercoding region sequences, for instance we use the regionin the mel operon from which we derived the tyrosinase melc1-melc2 geneswhich we have shown to be expressed at high levels in E. coli under thecontrol of a strong (tac) promoter. Genes could also be expressed andinduced off of independent promoters, such as tac and arabinose. Formammalian expression systems, single plasmid systems can be used forboth transient or stable cell line expression and for constitutive orinducible expression. Further, differential control of the expression ofone of the complementary fragment fusions, usually the bait-fusedfragment, can be controlled to minimize expression. This will beimportant in reducing background non-specific interactions. Examples ofdifferential control of complementary fragment expression include thefollowing strategies:

i) In polycistronic expression, transient or stable, expression of thesecond gene will necessarily be less efficient and so this in itselfcould serve to limit the quantity of one of the complementary fragments.Alternatively, the first gene product can be limited in expression bymutation of an upstream donor/splice site, while the second gene can beput under the control of a retroviral internal initiation site, such asthat of ECMV to enhance expression.ii) Individual complementary fragment-fusion pairs can also be put underthe control of inducible promoters, all commercially available includingthose based on Tet-responsive PhCMV*-1 promoter, and/or steroid receptorresponse elements. In such a system the two complementary fragment genescan be turned on and expression levels controlled by dose dependentexpression with the inducer, in these cases tetracycline and steroidhormones.

Example 2 Applications of the PCA Strategy to Detect Novel Gene Productsin Biochemical Pathways and to Map Such Pathways

Among the greatest advantage of PCA over other molecular interactionscreening methods is that they are designed to be performed both in vivoand in any type of cell. This feature is crucial if the goal of applyinga technique is to identify novel interactions from libraries andsimultaneously be able to determine if the interactions observed arebiologically relevant. The detailed example given below, and otherexamples at the end of this section illustrate how it is that validationof interactions with PCA is possible. In essence, this is achieved asfollows. In biochemical pathways, such as hormone receptor-mediatedsignaling, a cascade of enzyme-mediated chemical reactions are triggeredby some molecular event, such as by hormone binding to its membranesurface receptor. Enzyme interactions with protein substrates andprotein-protein or protein-nucleic acid interactions withenzyme-modified substrates then occur. Such biochemical signalingcascades only occur in specific cell types and model cell lines forstudying these processes. Therefore, to detect induced interactions,such as with known proteins in a pathway with yet unidentified proteins,one obviously needs to perform such screening in appropriate model celllines and in the correct cellular compartment. Only the PCA strategy canbe used in a general way to do this. Protein-molecular interactiontechniques such as yeast two- or three-hybrid techniques cannot beperformed in a context where such events occur, except in the limitingcase of nuclear interaction in yeast or interactions that are nottriggered. There do exist mammalian two-hybrid techniques where it mightbe possible to detect induced protein interactions, but only again ifthe proteins involved can be simultaneously activated, transported tothe nucleus and interact with their partners. PCAs do not have theselimitation since they do not require additional cellular machineryavailable only in specific compartments. A further point is that byperforming the PCA strategy in appropriate model cell types, it is alsopossible to introduce appropriate positive and negative controls forstudying a particular pathway. For instance, for a hormone signalingpathway it is likely that hormone signaling agonists and antagonists ordominant-negative mutants of signaling cascade proteins would be known,that are upstream or act in parallel to the events being examined in thePCA. These reagents could be used to determine if novel interactionsdetected by the PCA are biologically relevant. In general then,interactions that are detected only if hormone is introduced but are notseen if an antagonist is simultaneously introduced could be hypothesizedto represent interactions relevant to the process under study.

Below is a detailed description of an application of the DHFR thatillustrates these points, as well as further examples where the PCAstrategy could be used.

Application of the DHFR PCA to Mapping Growth Factor-Mediated SignalTransduction Pathways

One of the earliest detectable events in growth factor-activated cellproliferation is the serine phosphorylation of the S6 protein of the 40Sribosomal subunit. The discovery of serine/threonine kinases thatspecifically phosphorylate S6 have considerably aided in identifyingnovel mitogen mediated signal transduction pathways. Theserine/threonine kinase p70S6k has been identified as a specific S6phosphorylase¹³¹⁻¹³⁶. p70S6k is activated by serine and threoninephosphorylation at specific sites in response to several mitogenicsignals including serum in serum starved cells, growth factors includinginsulin and PDGF, and by mitogens such as phorbol esters. Considerableeffort has been made over the last five years to determine howp70/p85S6k are activated in response to mitogens. Two receptor-mediatedpathways have been implicated in p70S6k activation, one associated withthe phosphatidylinositol-3-kinase (PI(3)k) and the other with the PI(3)khomologue mTOR¹³⁷⁻¹⁴⁴. Key to understanding of this proposal, is thefact that the role of these enzymes in activation of p70S6k wasdetermined by effects of two natural products on phosphorylation andenzyme activity: rapamycin, which indirectly inhibits mTOR activity, andwortmannin, which directly inhibits PI(3)_(k) activity. It is alsoimportant to note that no direct upstream kinases or other regulatoryproteins of p70S6k have been identified to this date.

The interactions of p70S6k with its known substrate S6 can be studied asa test system for the DHFR PCA in E. coli and in mammalian cell lines.One can also seek to identify novel interactions with this enzyme thatwould lead to new insights into how this important enzyme is regulated.Also, since activation of the enzyme is mediated by multiple pathwaysthat can be selectively inhibited with specific drugs, this is an idealsystem to test PCAs as methods to distinguish induced versusconstitutive protein-protein interactions.

a) Testing of the E. coli Survival Assay: Interaction of p70S6k with S6

This test is ideal, because the apparent Km (=250 nM) of p70S6k for S6protein¹⁴⁵ is approximately the same as the Kd for leucinezipper-forming peptides from GCN4 used in our test system. However, wewill have to use a constitutively active form of the enzyme for ourtests. An N-terminal truncated form of the enzyme D77-p70S6k, isconstitutively active and will be used in these studies147.

Methodology: D77-p70S6k-F[1,2] fusion and D77-p70S6k-F[3] fusion, orF[1,2] and D77-p70S6k-F[3] fusion (as a control) will be cotransformedinto E. coli and the cells grown in minimal medium in the presence oftrimethoprim. Colonies will be selected and expanded for analysis ofkinase activity against 40S ribosomal subunits, and for coexpression ofthe two proteins.

b) Modification of the Bacterial Survival Assay for Library Screening:Identification of Novel Interacting Proteins.

Screening an expression library for interactions with a given target(p70S6k-D77, in this case) will be straightforward in this system, giventhat the only steps involved are: 1-construction of thefusion-expression library as a fusion with mDHFR fragment[3];2-transformation of the library in E. coli BL21 harboring pRep4 (forconstitutive expression of the lac repressor; this is required in thecase where a protein product is toxic to the cells) and a plasmid codingfor the fusion: p70S6k-D77-[1,2]; 3-plating on minimal medium in thepresence of trimethoprim and IPTG; 4-selection of any colonies thatgrow, propagation and isolation of plasmid DNA, followed by sequencingof DNA inserts; 5-purification of unknown fusion products via thehexaHis-tag and sizing on SDS-PAGE.

Methodology:

The overall strategy is illustrated in FIG. 5. 1-Construction of adirectional fusioN-expression library: i-cDNA production: One canisolate poly(A)+ RNA from BA/F3 cells (B-lymphoid cells) because thesecells have successfully been used in the study of therapamycin-sensitive p70S6k activation cascade¹³⁹. To enrich forfull-length mRNA, we will affinity purify the mRNA via the 5′ capstructure by the CAPture method¹⁴⁸. Reverse transcription will be primedby a “Linker Primer”: it has a poly(T) tail to prime from the poly(A)mRNA tail, and an XhoI site for later use in directional subcloning ofthe fragments. The first strand is then methylated. After second strandsynthesis and blunting of the products, “EcoRI Adapters” are added,producing digestion of the linkers with EcoRI and XhoI (the inserts areprotected by methylation) produces full-length cDNA ready fordirectional insertion in a vector opened with EcoRI and XhoI. Becausethe success of library screening depends largely on the quality of thecDNA produced, we will use the above methods as they have proven toconsistently produce high-quality cDNA libraries. ii-Insertion of thecDNA into vectors: The library will be constructed as a C-terminalfusion to mDHFR F[3] in vector pQE-32 (Qiagen), as we have obtained highlevels of expression of mDHFR fusions from this vector in BL21 cells.Three such vectors will be created, differing at their 3′ end, which isthe novel polycloning site that we engineered (described earlier, underMethods), carrying either 0, 1, or 2 additional nucleotides. This allowsread-through from F[3] into the library fragments in all 3 translationalreading frames. The cDNA fragments will be directionally inserted at theEcoRI and XhoI sites in all three vectors at once. 2, 3, 4, and 5—Thesesteps have been described earlier, under Results, apart from the finalsequencing of clones identified using sequencing primers specific tovector sequences flanking sites of library insertion. The proteinpurification will also be as described earlier, by a one-steppurification on Ni-NTA (Qiagen). If the product size is more than 15 kDaover the molecular weight of the DHFR component (equal to a cDNA insertof more than 450 bp), we will have the inserts sequenced at the SheldonBiotechnology Center (McGill University).

c) Development of the Eukaryotic Assay

The transformation of the system described above, is useful to producean equivalent assay for use in eukaryotic cells. The basic principle ofthe assay is the same: the fragments of mDHFR are fused to associatingdomains, and domain association is detected by reconstitution of DHFRactivity in eukaryotic cells (FIG. 5).

Creation of the expression constructs: The DNA fragments coding for theGCN4-zipper-mDHFR fragment fusions were inserted as one piece into pMT3,a eukaryotic transient expression vector¹²⁶. Expression of the fusionproteins in COS cells was apparent on SDS-PAGE after 35[S]Met labeling.Survival assays in eukaryotic cells: Two systems can be used fordetection of mDHFR reassembly, in parallel: i—CHO-DUKX B11 cells(Chinese Hamster Ovary cell line deficient in DHFR activity) arecotransfected with GCN4-zipper-mDHFR fragment fusions. The cells aregrown in the absence of nucleotides; only cells carrying reconstitutedDHFR will undergo normal cell division and colony formation.ii-Methotrexate (MTX)-resistant mutants of mDHFR have been created, withthe goal of transfecting cells that have constitutive DHFR activity suchas COS and 293 cells. We mutated F[1,2] in order to incorporate, one ata time, each of five mutations that significantly increase Ki (MTX):Gly15Trp, Leu22Phe, Leu22Arg, Phe31Ser and Phe34Ser (numbering accordingto the wild-type mDHFR sequence). These mutations occur at varyingpositions relative to the active site and relative to F[3], and havevarying effects on Km (DHF), Km (NADPH) and Vmax of the full-lengthmammalian enzymes in which they were. Mutants Z-F[1,2: Leu22Phe],Z-F[1,2: Leu22Arg] and Z-F[1,2: Phe31Ser] all allowed for bacterialsurvival with high growth rates when cotransformed with Z-F[3] (resultsnot shown). The five mutants will be tested in eukaryotic cells, inreconstitution of mDHFR fragments to produce enzyme that can sustain COSor 293 cell growth while under the selective pressure of MTX, which willeliminate background due to activity of the native enzyme. The mutationsoffers an advantage in selection while presenting no apparentdisadvantage with respect to reassembly of active enzyme. If thereconstituted mDHFR produced in either of the survival assays allowseukaryotic cell growth that is significantly slower than growth with thewild-type enzyme, thymidylate will be added to the growth medium topartially relieve the selective pressure offered by the lack ofnucleotides.

d) Testing of the Eukaryotic Survival Assay

It is necessary at the outset to test whether induced interactions withp70S6k can be detected. One can use the same test system as that for theE. coli test system described above: Induction of association of p70S6kwith S6 protein.

Methodology:

mDHFR Leu22Phe mutant S6-F[1,2] and p70S6k-F[3], or F[1,2] andp70S6k-F[3] (as a control) will be cotransfected into COS cells and thecells will be serum starved for 48 hours followed by replating of cellsat low density in serum and MTX. Colonies will be selected and expandedfor analysis of kinase activity against 40S ribosomal subunits, and forcoexpression of the two proteins. Further controls will be performed forinhibition of protein association with wortmannin and rapamycin.

e) Modification of the Eukaryotic Survival Assay for Library Screening

An important part of the work required in creating a library for use ineukaryotic cells will have been accomplished already, as the EcoRI/XhoIdirectional cDNA produced by the Stratagene “cDNA Synthesis Kit” candirectly be inserted directionally into the Stratagene Zap Expressvector.

Methodology:

Steps 1 through 5 are parallel to those for the bacterial libraryscreening (above). 1—Again, the library is constructed as a C-terminalfusion to mDHFR F[3]. F[3] (with no stop codon) will be inserted inframe in Zap Express, followed by insertion of the novel polylinkersallowing expression of the inserts in all three reading frames(described above), and by the EcoRI/XhoI directional cDNA. Thisbacteriophage library will be propagated and treated with the Stratagenehelper phage to excise a eukaryotic expression phagemid vector (pBK-CMV)carrying the fusion inserts. 2—Cotransfection of the library andp70S6k-F[1,2] constructs in eukaryotic cells: we will perform thescreening in COS or 293 cells, as these are responsive to serum inactivating the p70S6k signaling pathway. Selection experiments will beperformed as described for the S6 test system above. 3—Propagation,isolation and sequencing of the insert DNA will be undertaken. 4—Thecloned fusion proteins will be sized on SDS-PAGE by direct visualizationafter 35S-Met/Cys labeling, or by Western blotting using a commercialpolyclonal antibody to mDHFR.

Generalization of the Strategy: The scheme for detecting partners forthe protein p70S6k can be applied to studies of any biochemical pathwayin any living organism. Such pathways may also be related to diseaseprocesses. The disease-related pathway may be an intrinsic process ofcells in humans where a pathology arises from, for instance mutation,deletion or under or over expression of a gene. Alternatively thebiochemical pathway may be one that is specific to a pathogenic organismor the mechanism of host invasion. In this case, component proteins ofsuch processes may be targets of a therapeutic strategy, such asdevelopment of drugs that inhibit invasion by the organism or acomponent enzyme in a biochemical pathway specific to the pathogenicorganism.

Inflamatory diseases are a case in point that can concern both examples.The protein-protein interactions that mediate the adhesion of leukocytesto inflamed tissues are known to involve such proteins as vascular celladhesion molecule-1 (VCAM-1), and certain cytokines such as IL-6 andIL-8 that are produced during inflammation. However, many of theproteins involved in onset of inflammatory response remain unknown;further, the intracellular signaling pathways triggered by theextracellular associations are poorly understood. The PCAs could be usedin elucidation of the mechanisms underlying the onset of inflammation,as well the ensuing signaling. For example, signaling pathwaysassociated with inflammation, such as those mediated by IL-1, IL-6, IL-8and tumor necrosis have been studied in some detail and many direct anddownstream regulators are known. These regulators can be used asstarting point targets in a PCA screening to identify other signallingor modulating proteins that could also be targets for drug development.

There is an increased risk of infection by enteric pathogens in theoccurrence of the intestinal inflammation that characterizes idiopathicintestinal diseases. There are two mechanisms which need to be betterunderstood here and which can be addressed by PCA:

i—the cellular mechanisms of inflammation as described above, andii—the discovery of the specific cell-surface ligands which thepathogenic organisms recognize and associate with. Secreted proteinsproduced by the pathogen can bind to the basolateral membrane ofepithelial cells (as in the case in Yersinia pseudotuberculosisinfection) or be translocated into intestinal epithelial cells(Salmonella infection), promoting infectivity and/or physiologicalresponses to the infection. However, in most cases the interactionsbetween the pathogenic protein and the epithelial cells are unknown.Cell adhesion and nervous system regeneration A related example in celladhesion includes processes involved in development and regeneration inthe nervous system. Cadherens are membrane proteins that mediatescalcium dependent cell-cell adhesion. To do so they need another classof cytoplasmic proteins called cathenins. Those make a bridge betweencadherins and cytoskeleton. Cathenins are also regulate genes thatcontrol differentiation-specific genes. For instance, the proteinB-cathenin can interact in certain situation with a transcription factor(lef-1) and be translocated into the nucleus where it constrains thenumber of genes transactivated by lef-1 (differentiation). This processis regulated by the Wnt signaling pathway (homologs to the winglesspathway in drosophila) by inactivation of GSK3B which permit degradationafter of APC (a cytoplasmic adapter protein). PCA strategies could beused to identify novel proteins involved in the regulation of theseprocesses.

Proteins involved in viral integration processes are examples of targetsthat could be tested for inhibitors using the PCA strategies. Examplesfor the HIV virus include:

i) inhibition of integrase or the transport of the pre-integrationcomplex: protein Ma or vpr.ii) Inhibition of the cell cycle in G2 by vpr (interaction by cyclin B)causing induction of apoptosis.iii) Inhibition of the interaction of gp160 (precursor of the membraneproteins) with furine.Accessory proteins of HIV as a therapeutic target:i) Vpr: nuclear localizing sequence (target): interaction site of vprwith phosphatasesA.ii) vif: interaction with vimentin (cytoskeleton associated protein).ii) Vpu: Degradation of CD4 in the RE mediated by the cytoplasmic tailof Vpu.iii) net Myristoylation signal of Nef.

Example 3 Other Examples of Protein Fragment Complementation Assays

Other examples of assays are herein exemplified. The reason to producethese assays is to provide alternative PCA strategies that would beappropriate for specific protein association problems such as studyingequilibrium or kinetic aspects of assembly. Also, it is possible that incertain contexts (for example, specific cell types) or for certainapplications, a specific PCA will not work but an alternative one will.Further below are brief descriptions of each other PCAs embodiments.

1) Glutathione-S-Transferase (GST) GST from the flat worm Schistosomajaponicum is a small (28 kD), monomeric, soluble protein that can beexpressed in both prokaryotic and eukaryotic cells. A high resolutioncrystal structure has been solved and serves as a starting point fordesign of a PCA. A simple and inexpensive colorimetric assay for GSTactivity has been developed consisting of the reductive conjugation ofreduced glutathione with 1-chloro-2,4-dinitrobenzene (CNDB), a brilliantyellow product. We have designed a PCA based on similar structuralcriteria used to develop the DHFR PCA using GCN4 leucine zippers asoligomerization domains. Cotransformants of zipper-GST-fragment fusionsare expressed in E. coli on agar plates and colonies are transferred tonitrocellulose paper. Detection of fragment complementation is detectedin an assay where a glutathione-CDNB reaction mixture is applied as anaerosol on the nitrocellulose and colonies expressing co-expressedfragments of GST are detected as yellow images.2) Green Fluorescent Protein (GFP) GFP from Aequorea victoria isbecoming one of the most popular protein markers for gene expression.This is because the small, monomeric 238 amino-acids protein isintrinsically fluorescent due to the presence of an internal chromophorethat results from the autocatalytic cyclization of the polypeptidebackbone between residues Ser65 and Gly67 and oxidation of the—bond ofTyr66. The GFP chromophore absorbs light optimally at 395 nm andpossesses also a second absorption maximum at 470 nm. This bi-specificabsorption suggests the existence of two low energy conformers of thechromophore whose relative population depends on local environment ofthe chromophore. A mutant Ser65Thr that eliminates isomerization (singleabsorption maximum at 488 nm) results in a 4 to 6 times more intensefluorescence than the wild type. Recently the structure of GFP has beensolved by two groups, making it now a candidate for a structure-basedPCA-design, which we have begun to develop. As with the GST assay, weare doing all of our initial development in E. coli with GCN4 leucinezipper-forming sequences as oligomerization domains. Direct detection offluorescence by visual observation under broad spectrum UV light will beused. We will also test this system in COS cells, selecting forco-transfectants using fluorescence activated cell sorting (FACS).3) Fire Fly Luciferase. Firefly luciferase is a 62 kDa protein whichcatalyzes oxidation of the heterocycle luciferin. The product possessesone of the highest quantum yields for bioluminescent reactions: onephoton is emitted for every oxidized luciferin molecule. The structureof luciferase has recently been solved, allowing for structure-baseddevelopment of a PCA. As with our GST assay, cells are grown on anitrocellulose matrix. The addition of the luciferin at the surface ofthe nitrocellulose permits it to diffuse across the cytoplasmicmembranes and trigger the photoluminescent reaction. The detection isdone immediately on a photographic film. Luciferase is an idealcandidate for a PCA: the detection assays are rapid, inexpensive, verysensitive, and utilizes non-radioactive substrate that is availablecommercially. The substrate of luciferase, luciferin, can diffuse acrossthe cytoplasmic membrane (under acidic pH), allowing the detection ofluciferase in intact cells. This enzyme is currently utilized as areporter gene in a variety of expression systems. The expression of thisprotein has been well characterized in bacterial, mammalian, and inplant cells, suggesting that it would provide a versatile PCA.4) Xanthine-guanine phosphoribosyl transferase (XGPRT) The E. colienzyme XGPRT converts xanthine to xanthine monophosphate (XMP), aprecursor of GMP. Because the mammalian enzyme hypoxanthine-guaninephosphoribosyl transferase HGPRT can only use hypoxanthine and guanineas substrates, the bacterial XGPRT can be used as a dominant selectionassay for a PCA for cells grown in the presence of xanthine. Vectorsexpressing XGPRT confer the ability of mammalian cells to grow inselective medium containing adenine, xanthine, and mycophenolic acid.The function of mycophenolic acid is to inhibit de novo synthesis of GMPby blocking the conversion of IMP into XMP (Chapman A. B., (1983) Molec.& Cellul. Biol. 3, 1421-1429). The only GMP produced then come from theconversion of xanthine into XMP, catalyzed by the bacterial XGPRT. Aswith aminoglycoside phosphotransferase fragments of XGPRT can begenerated based on the known structure (See table 1.) using thedesign-evolution strategy described above with fragments fused to theGCN4 leucine zippers as a test oligomerization domains. Thecomplementary fusions are cotransfected and the proteins transientlyexpressed in COS-7 cells, or stability expressed in CHO cells, grown inthe selective medium. In the case of CHO cells, colonies are collectedand sequentially re-cultured at increasing concentrations of theselective compounds in order to enrich for populations of cells thatefficiently express the fusions at high concentrations.5) Adenosine deaminase Adenosine deaminase (ADA) is present in minutequantities in virtually all mammalian cell. Although it is not anessential enzyme for cell growth, ADA can be used in a dominantselection assay. It is possible to establish growth conditions in whichthe cells require ADA to survive. ADA catalyzes the irreversibleconversion of cytotoxic adenine nucleosides to their respective nontoxicinosine analogues. By adding cytotoxic concentrations of adenosine orcytotoxic adenosine analogues such as 9-b-D-xylofuranosyladenine to thecells, ADA is required for cell growth to detoxify the cytotoxic agent.Cells that incorporate the ADA gene can then be selected foramplification in the presence of low concentrations of2′-deoxycoformycin, a tight-binding transition state analogue inhibitorof ADA. ADA can then be used for a PCA based on cell survival (Kaufman,R. J. et al. (1986) Proc. of the Nat. Acad. Sci. (USA) 83, 3136-3140).As with the other systems described above, fragments of ADA can begenerated based on the known structure (See table 1.) using thedesign-evolution strategy described above with fragments fused to theGCN4 leucine zippers as a test oligomerization domains. Thecomplementary fusions are cotransfected and the proteins transientlyexpressed in COS-7 cells, or stability expressed in CHO cells, grown inthe selective medium containing 2′-deoxycoformycin. In the case of CHOcells, colonies are collected and sequentially re-cultured at increasingconcentrations of 2′-deoxycoformycin in order to enrich for populationsof cells that efficiently express the fusions at high concentrations6) Bleomycin binding protein (zeocin resistance gene) Zeocin, a memberof the bleomycin/phleomycin family of antibiotics, is toxic to bacteria,fungi, plants, and mammalian cells. The expression of the zeocinresistance gene confers resistance to bleomycin/zeocin. The proteinconfers resistance by binding to and sequestering the drug and thuspreventing its association and hydrolysis of DNA. Berdy, J. (1980) InAmino Acid and Peptide Antibiotics, J. Berdy, ed. (Boca Raton, Fla.: CRCPress), pp. 459-497; Mulsant, P., Tiraby, G., Kallerhoff, J., andPerret, J. (1989 Somat. Cell. Mol. Genet. 14, 243-252). Bleomycinbinding protein (BBP) could then be used for a PCA based on cellsurvival. As with the other systems described above, fragments of ADAcan be generated based on the known structure (See table 1.) using thedesign-evolution strategy described above with fragments fused to theGCN4 leucine zippers as a test oligomerization domains. The BBP is asmall (8 kD) dimer that binds to drugs via a subunit interface bindingsite. For this reason, the design would be somewhat different in thatfirst, a single chain form of the dimer would be generated by making afusion of two BBP genes with a short sequence coding for a simplepolypeptide linker introduced between the two subunits. Fragments inthis case will be based on a short sequence of one of the subunitmodules, while the other fragment will be composed of the remainingsequence of the subunit plus the other subunit. Complementation andselection experiments will be performed as described for the examplesabove using bleomycin or zeocin as selective drugs.7) Hygromycin-B-phosphotransferase. The antibiotic hygromycin-B is anaminocyclitol that inhibits protein synthesis by disruptingtranslocation and promoting misreading. The E. coli enzymehygromycin-B-phosphotransferase detoxifies the cells by phosphorylatingHygromycin-B. When expressed in mammalian cells,hygromycin-B-phosphotransferase can confer resistance to hygromycin-B(Gritz, L., and Davies, J. (1983) Gene 25, 179-188.). The enzyme is adominant selectable marker and could be used for a PCA based on cellsurvival. While the structure of the enzyme is not known it is suspectedthat this enzyme is homologous to aminoglycoside kinase (Shaw, et al.(1993) Microbiol. Rev. 57, 138-163). It is therefore possible to use thecombined design/evolution strategy to produce a PCA with this enzyme andperform dominant selection in mammalian cells with selection atincreasing concentrations of hygromycin B.8) L-histidinol NAD+oxydoreductase. The hisD gene of Salmonellatyphimurium codes for the L-histidinol NAD+oxydoreductase that convertshistidinol to histidine.

Mammalian cells grown in media lacking histidine but containinghistidinol can be selected for expression of hisD (Hartman, S. C., R. C.Mulligan (1988) Proc. of the Nat. Acad. Sci. (USA) 85, 8047-8051). Anadditional advantage of using hisD in dominant selection is thathistidinol is itself toxic, inhibiting the activity of endogenoushistidyl-tRNA synthetase. Histidinol is also inexpensive and readilypermeates cells. The structure of histidinol NAD+oxydoreductase isunknown and so development of a PCA based on this enzyme is basedentirely on the exonuclease fragment/evolution strategy. The followingTable list alternative embodiments using other PCA reporters.Abbreviations in Table: Type: D, dominant selection marker; R, recessiveselection marker. Structure: four letter codes=Protein Data Bank (PDB)entries; K, known but not deposited in PDB; U, unknown. mono/oligo: M,monomer; D, dimer; tetra, tetramer.

TABLE 1 A list of Other Potential PCA Reporter Candidates A-Assays basedon Dominant or Recessive Selection mono/ Enzyme Type Structure Sizeoligo Selection drugs/Conditions DHFR R/D many 18 kD Mmethotrexate/trimethoprim Adenosine deaminase D/R 1ADD M Xyl-A oradenosine, alanosine, and 2′- deoxycoformycin Thymidine kinase D/R 1KIND gangcyclovene, HAT Mutant hypoxanthine- guanine D 1HGM D HAT +thymidine kinase phosphoribosyl transferase Thymidylate synthetase R1NJE 35 kd M 2 fluorodeoxyuridine Xanthine-guanine D 1NUL mycophenolicacid with phosphoribosyl transferase limiting xanthine Glutaminesynthetase R 2LGS Asparagine synthetase R U B-aspartyl hydroxamate oralbizin Puromycin N-acetyltransferase D U 23 kD M puromycinAminoglycoside D K 35 kD M neomycin, G418, gentamycin phosphotransferaseHygromycin B D U M hygromycin B phosphotransferase L-histidinol: NAD+ DU 46 kD M histidinol oxidoreductase Bleomycin binding protein D K 8 kD Dbleomycin/zeocin Cytosine methyl-transferase R/D U 5-Azacytidine(5-aza-CR) and 5-aza-2′-deoxycytidine O6-alkylguanine D 1ADNN-methyl-N-nitrosourea alkyltransferase Glycinamide ribonucleotide R1GRC 23.2 kD D dideazatetrahydrofolate, transformylase minus purineGlycinamide ribonucleotide R U 45.9 kD minus purine synthetasePhosphoribosyl-aminoimidazole R U 36.7 kD minus purine synthetaseFormylglycinamide ribotide R U 141.4 kD M L-azaserine, 6-diazo-5-oxo-amidotransferase L-norleucine, minus purinePhosphoribosyl-aminoimidazole R U 39.5 kD D minus purine carboxylasePhosphoribosyl-aminoimidazole R U 57.3 kD minus purine carboxamideformyltransferase Fatty acid Synthase R 272 kD D cerulenin IMPdehydrogenase R 1AK5 55.4 kD Tetra mycophenolic acid Mono/ Enzyme TypeStructure Size Oligo Selection drugs/Conditions ii-Viral Plaque AssaysThioredoxin D 1TDF 34.5 kD D Reverse transcriptase D 3HVT Viral proteaseD B-Cell Death Assays Cysteine protease: papain D 1STF 38.9 kD Minhibited by cystatin Cysteine protease: caspase D 1CP3 17 kD + HeteroDinhibited by DEVD-aldehyde 12 kD (can also by used in a fluorimetric orcolorimetric assay, in vitro) Metalloprotease: D 47.1 kD M inhibited bymethyl-ethyl carboxypeptidase succinic acid Serine protease: proteinaseD 1PTK 30.6 kD M inhibited by serpins K Aspartic protease: pepsin D 1PSN34.5 kD M inhibited by pepstatin A (can also be used in an fluorimetricassay, in vitro) Lysozyme D many 23.2 kD M inhibited by N-acetylglucosamine trisaccharide RNAse D many 13.3 kD M inhibited byRNAse inhibitor DNAse D 1DNK 61.6 kD M inhibited by actin PhospholipaseA2 D 1P2P 13.8 kD M/D many inhibitors: bromophenacyl bromide, hexadecyl-trifluoroethyl-glycero- phosphomethanol, bromoenol lactone, etc.Phospholipase C D 1AH7 28 kD M many inhibitors: neomycin, chelerythrine,U73122, etc. Mono/ Enzyme Structure Size Oligo Selectiondrugs/Conditions C-Colorimetric/Fluorimetric Assay DT-Diaphorase(NAD(P)H- 1QRD 26 kD D NADPH-diaphorase stain, inhibited [quinoneacceptor] by dicumarol, Cibacron blue and oxidoreductase) phenidioneNote: can also be used in a cell death assay (+nitrobenzimidazole, foexample). (NAD(P)H-[quinone acceptor] isoform of 21 kD D NRH-diaphorasestain, inhibited by oxidoreductase)-2 1QRD pentahydroxyflavoneThermophilic diaphorase 30 kD M NADH-diaphorase stain (Bacillusstearothermophilus) Glutathione-S-transferase 1GNE 26 kD D production ofa yellow product by other the conjugation of glutathione with isoform anaromatic substance, chloro of dinitrobenzene (CDNB) 28 kD Luciferase1LCI 62 kD M Fluorometric Green-fluorescent protein 1EMA 30 kD MIntrinsic fluorescence Chloramphenicol 1CLA 25 kD Tri Fluorimetric:Bodipy acetyltransferase chloramphenicol Uricase 32 kD TetraFluorometric SEAP (secreted form of human 1AJA M CSPD chemiluminescentsubstrate placental alkaline phosphatase) B-Glucuronidase 1BHG 71 kDTetra Histochemical, fluorometric or spectrophotometric assays usingvarious substrates such as X-GLUC. D-Heteromeric Enzyme StrategiesTyrosinase 30 kD + Hetero Colorimetric: synthesis of melanin 14 kD M + M

Example 4 Examples of Variants of PCA to Detect MultipleProtein/Protein-DNA/Protein RNA/Protein-Drug Complexes

To this point specific examples have only been made of applications ofPCA to protein-pair interactions. However, it is possible to apply PCAto multiprotein, protein-RNA, protein-DNA or protein-small moleculeinteractions. There are two general schemes for achieving such systems.Multi-subunit PCA: Two proteins need not interact for a PCA signal to beobserved; if a partner protein or protein complex binds to two proteinssimultaneously, it is possible to detect such a three protein complex. Amultusubunit PCA is conceived with the example of herpes simplex virusthymidine kinase (TK), a homodimer of 40 kD. In this conception, the TKstructure contains two well defined domains consisting of an alpha/beta(residues 1-223) and an alpha-helical domain (224-374). As a testsystem, we use the Rop1 dimer, a four helix bundle homodimer. The twofragments of TK are extracted by PCR and subcloned into the transienttransfection vector pMT3, the first in tandem to the Adenovisus majorlate promoter, tripartite leader 3′ to the first ATG, and the seconddownstream of a ECMV internal initiation site. Restriction sitespreviously introduced between the first and the last ATG are subclonedinto BamHI/KpnI and PstI/EcoRI cloning sites downstream of the two ATGs.These are used to subclone PCR-generated fragments of the Rop1 subunitsinto two different vectors. Subsequently Ltk-cells are cotransfected bylipofection with the two plasmids and colonies of surviving cells areserially selected in medium containing increasing concentrations of HAT(hypoxanthine/aminopterin/thymidine). Cells that express complementaryfragments of TK fused to the four Rop1 will proliferate under thisselective pressure, or otherwise die. Specific examples of use of thisconcept would be in determining constituents of multiprotein complexesthat are formed transiently or constitutively in cells.

The utility of PCA is not limited to detecting protein-proteininteractions, but can be adapted to detecting interactions of proteinswith DNA, RNA, or small molecules. In this conception, two proteins arefused to PCA complementary fragments, but the two proteins do notinteract with each other. The interaction must be triggered by a thirdentity, which can be any molecule that will simultaneously bind to thetwo proteins or induce an interaction between the two proteins bycausing a conformational change in one or both of the partners. Twoexamples have been demonstrated in our lab using the mDHFR PCA in E.coli. In the first case a natural product, the immunosuppressant drugrapamycin, is used to induce an interaction between its receptor FKBP12and a partner protein mTOR (mammalian Target of Rapamycin). We detectthis by cotransformation of DHFR fragments fused to FKBP or mTOR into E.coli grown in the presence or absence of trimethoprim (as describedabove) and rapamycin (0-10 nM). We have demonstrated that support ofgrowth as detected by colony formation is completely dependent on theaddition of rapamycin, suggesting that the mDHFR PCA is detecting arapamycin-induced assembly of a FKBP12-mTOR and subsequentreconstitution of DHFR activity. This is one example of a use of the PCAstrategy to test for small molecules that can induce interactionsbetween proteins. General applications could be made to therapeuticdevelopment, in the form screening small molecule combinatorial compoundlibraries for molecules that induce interactions between proteins, thatmay inhibit the activities of either or both of the proteins, oractivate specific cellular processes that are initiated by other events,such as growth factor-mediated receptor dimerization. The discovery ofsuch small molecules could lead to the development of orally availabledrugs for the treatment of a broad spectrum of human diseases.

Another example of an induced interaction we have studied with the DHFRPCA is the interaction of the oncogene GTPase p21 ras and its directdownstream target, the serine/threonine kinase raf. This interactiononly occurs when the GTPase is in the GTP-bound form, whereas turnoverof GTP to GDP leads to release of the complex. As with the FKBP-mTORcomplex, we have demonstrated this induced interaction in E. coli. PCAcould be used in a general way to study such induced interactions, andto screen for compounds that release or prevent these interactions inpathological states. The ras-raf interaction itself could be a target oftherapeutic intervention. Oncogenic forms of ras consist of mutants thatare incapable of turning over GTP and therefore remain continuouslyassociated with activated ras. This leads to a constitutive uncontrolledgrowth signal that results, in part, in oncogenesis. The identificationof compounds that inhibit this process, by PCA, would be of value inbroad treatment of cancers. Other examples of multimolecularapplications of PCA could include identification of novel DNA or RNAbinding proteins. In its simplest conception one uses a known DNA or RNAbinding motifs, for instance a retinoic acid receptor zinc finger, or asimple RNA binding protein such as IF-1, respectively. One half of thePCA consists of the DNA or RNA protein binding domain fused to one ofthe PCA fragments (control fragment). The complementary fragment isfused to a cDNA library. A third entity, the gene coding for a sequencecontaining an element known to bind to the control protein, and then asecond putative or known regulatory element is coded for after thissequence. A test system consists of tat/tar elements that controlelongation in transcription/translation of HIV genes. An exampleapplication would be identification of tat binding elements that havebeen proposed to exist in eukaryotic genomes and may regulate genes inthe same or similar way to that of HIV genes. (SenGupta D. J. et al.(1996) Proc. Natl. Acad. USA 6, 8496-8501).

Example 5 Examples of PCA Applications to Drug Screening ScreeningCombinatorial Libraries of Compounds for Those that Inhibit or InduceProtein-Protein/Protein-rna/Protein-DNA Complexes A) Drug Screening.

Screening combinatorial libraries of compounds for those that inhibit orinduce protein-protein/protein-rna/protein-DNA complexes. The PCAstrategy can be directly applied to identifying potentially therapeuticmolecules contained in combinatorial libraries of organic molecules. Itis possible to perform high throughput screening of such libraries toscreen for compounds that will inhibit or induce protein-proteininteractions or protein-DNA/RNA interactions (as discussed above). Inaddition it is also possible to screen for compounds that inhibitenzymes whose substrates are other proteins DNA, RNA or carbohydrates,as discussed below. In this application, proteins that interact/proteinsubstrate pairs, or control DNA/RNA binding protein-enzyme pairs arefused to PCA complementary fragments and plasmids harboring these pairsare transformed/transfected into a cell, along with any third DNA or RNAelement as the case requires. Transformed/transacted cells are grownliquid culture in multiwell plates where each well is inoculated with asingle compound from an array of combinatorially synthesized compounds.A readout of a response depends on the effect of a compound. If thecompound inhibits a protein interaction, there is a negative response(no PCA signal is the positive response). If the compound induces aprotein interaction, the response is a positive PCA signal. Controls fornon-specific effects of compounds include: 1) demonstration that thecompound does not effect the PCA enzyme itself (test against cellstransfected with the wild-type intact enzyme used as the PCA probe) andin the case of a cell survival assay, that the compound is not toxic tothe cells that have not been transformed/transfected. As well asproviding a high throughput assay for biological activity of compounds,PCA also offers the advantage over in vitro assays that it is a test forcell membrane permeability of active compounds. Specific demonstratedexamples of PCA for drug screening in our laboratory include theapplication of DHFR PCA in E. coli to detecting compounds that inhibittherapeutically relevant targets. These include Bax/Bcl2 fkbp12/torras/raf, carboxyl terminal dimerization domain of HIV-1 capsid protein,IkB kinase IKK-1 and IKK-2 dimerization domains (leucine zippers andhelix-loop-helix domains). In each case, the two proteins are subcloned5′ upstream of either F[1,2] or F[3] as described above. Plasmidsharboring the complementary fragments are cotransformed into BL21 cells.Colonies from minimal medium plates containing IPTG and trimethoprim arepicked, and grown in liquid medium under the same selective conditionsand frozen stocks made. For a single screening cycle, a primingovernight culture is grown from frozen stocks in LB medium. A selectiveminimal medium containing trimethoprim, ampicillin, IPTG is aliquated at25 ml into each well of a 384 well plate. Each well is then inoculatedwith 1 ul of an individual sample from a compound array (ArQule Inc.) togive a final concentration of 10 uM. Each well is then inoculated with 2ml of overnight culture and plates are incubated in a specially adaptedshaker bath at 37 C. At 2 hour intervals, plates are read on an opticalabsorption spectroscopic plate reader coupled to a PC and spreadsheetsoftware at 600 nm (scattering) for a period of 8 hours. Rates of growthare calculated from individual time readings for each well and comparedto a standard curve. A “hit” is defined as a case where an individualcompound reduces the rate of growth to less than the 95% confidenceinterval based on the standard deviation for growth rates observed inall of the wells within the test plate. “Near hits” are defined as thosecases where growth rates are within the 95% confidence interval. Foreach of the hits or near hits, the following controls are thenperformed: The same experiment is performed with BL21 cells that aretransformed with empty vector (and no trimethoprim), with vectorharboring the full length mDHFR gene, or with cotransfected cells whereprotein expression is not induced by IPTG. If in all of these cases thecompound has no effect, it can be concluded that it is specificallydisrupting the protein-protein interaction being tested. Such validatedhits or near hits are then retested to establish a dose-response curvefor the individual compound, with concentrations varying from 1 μM up to1 μM by orders of magnitude of 10. The PCA strategy for compoundscreening can also be applied in the multiprotein protein-RNA/DNA casesas described above, and can easily be adapted to the DHFR or any otherPCA in E. coli or in yeast versions of the same PCAs. Such screening canalso be applied to enzymes whose targets are other proteins or nucleicacids for known enzyme/substrate pairs or to novel enzyme substratepairs identified as described below.

Proteins involved in viral integration processes are examples of targetsthat could be tested for inhibitors using the PCA strategies. Examplesfor the HIV virus include:i) inhibition of integrase or the transport of the pre-integrationcomplex: protein Ma or vprii) Inhibition of the cell cycle in G2 by vpr (interaction by cyclin B)causing induction of apoptosis.iii) Inhibition of the interaction of gp160 (precursor of the membraneproteins) with furine.Accessory proteins of HIV as a therapeutic target:i) Vpr: nuclear localizing sequence (target): interaction site of vprwith phosphatasesA.ii) vif: interaction with vimentin (cytoskeleton associated protein).ii) Vpu: Degradation of CD4 in the RE mediated by the cytoplasmic tailof Vpu.iii) net Myristoylation signal of Nef.

Other general targets for drug screening could include proteins linkedneurodegenerative diseases, such as to alpha-synuclein. This protein hasbeen linked to early onset of Parkinson disease and it is present alsoimplicated in Alzheimer disease. There is also β-amyloid proteins,linked to Alzheimers disease.

An example of protein-carbohydrate interactions that would be a targetfor drug screening includes the selectins that are generally implicatedin inflammation. These cell surface glycoproteins are directly involvedin diapedesis.

A number of tumor suppressor genes whose actions are mediated byprotein-protein interactions could be screened for potential anti-cancercompounds. These include PTEN, a tumor suppressor directly involved inthe formation of harmatomas. It is also involved in inherited breast andthyroid cancer. Other interesting tumor suppressor genes include p53, Rband BARC1.

Example 6 Examples of Applications the PCA Strategy to DetectEnzyme/Substrate Interactions

The examples described above are used for identifying novel molecularinteractions involving molecules that merely bind to each other. Howeverdetecting the substrates of enzymes is also fully compatible with thePCA strategy as shown below:

i) Enzymes that form tight complexes or with protein substrates orinduce efficient PCA fragment assembly orii) Mutant enzymes that bind tightly to substrate but do not undergoproduct release because of mutations residues involved in nucleophilicattack and/or product release (substrate trapping).

Enzymes may form tight complexes with their substrates (Kd ˜1-10 μM). Inthese cases PCA may be efficient enough to detect such interactions.However, even if this is not true, PCA may work to detect weakerinteractions. Generally, if the rate of catalysis and product release isslower than the rate of folding—reassembly of the PCA complementaryfragments, effectively irreversible folding and reconstitution of thePCA reporter activity will have occurred. Therefore, even if the enzymeand substrate are no longer interacting, the PCA signal is detected.Therefore, the detection of novel enzyme substrates using PCA may bepossible, independent of effective substrate Kd or rate of productrelease. In cases where product release is much faster than PCA fragmentassembly/folding and alternative approach is provided by generating“substrate trapping” mutants of the test enzyme. An example of thisapproach applied to the protein tyrosine phosphatase PTP1B, wheresubstrate trapping mutants have been generated by mutating thenucleophilic aspartate 181 to alanine rendering the enzyme catalyticlydead, but capable of forming tight complexes with a known substrate, theEGF receptor and other unknown proteins (Flint, A. J. et al. (1996)Proc. Natl. Acad. USA 941680-1685). An application of using PCA toscreen for interacting partners of PTP1B is given as follows. We use theaminoglycoside kinase (AK)-based PCA in transiently transfected COS or293 cells. The substrate trap mutant catalytic domain of PTP1B is fusedto N-terminal complementary fragment of AK, while a C-terminal fusion ofthe other AK fragment is made to a cDNA library. Cells are cotransfectedwith complementary AK pairs and grown in selective concentrations ofG418. After 72 hours, colonies of surviving cells are picked and in situPCR is performed using primers designed to anneal to 3′ and 5′ flankingregions of the cDNA coding region. PCR amplified products are then 5′sequenced to identify the gene.

Enzyme inhibitors Screening combinatorial libraries of compounds forthose that inhibit enzyme-PROTEIN substrate complexes either with:i) Enzymes that form tight complexes with protein substrates orii) Mutant enzymes that bind tightly to substrate but do not undergoproduct release because of the mutation.

Example 7 Applications of the PCA Strategy to ProteinEngineering/Evolution

The PCA strategy can be used to generate peptides or proteins with novelbinding properties that may have therapeutic value, as is done todaywith phage display technology. It is also possible to develop enzymeswith novel substrate or physical properties for industrial enzymedevelopment. Two detailed examples of the application of the PCAstrategy to these ends are given below, with additional applicationslisted below.

1) Selection of high-affinity, heterodimerizing leucine zipper sequences(J. Pelletier, K. Arndt, A. Plueckthun and S. Michnick, manuscript inpreparation). The mDHFR PCA, described above, was used in a scheme forthe selection of efficiently heterodimerizing, designed leucine zippers.It has been proposed that the formation of salt bridges betweenpositively and negatively charged residues at complementing “e” and “g”positions is important in stabilizing leucine zipper formation, thoughthis view has been contested. In order to help define the importance ofsalt-bridge formation at the e and g positions, two leucine zipperlibraries were built. Both are based on the GCN4 leucine zippersequence, but contain sequence information specific to either Jun or Foszippers in order to create heterodimerizing pairs. As well, the e-1 toe-4 and g-1 to g-4 positions in each library were randomized to code forpositively or negatively charged residues, or neutral polar residues.These libraries were amplified by PCR and subcloned into the Z-F[1,2] orZ-F[3] constructs (described above) from which the GCN4 zipper sequenceshad been removed. The bacterial mDHFR PCA selection was performed onselective solid media, as described earlier. Colonies were picked andsequenced; sequence analysis reveals that the distribution of charged orneutral residues at e-g pairs is not random, but is biased towardpairing of opposite charges, or pairing of a charged with a neutralresidue, rather than same-charge pairing (see FIG. 7). We reasoned thatbetter zipper pairing should lead to an increase in efficiency ofDHFR-fragment complementation, resulting in faster bacterial doublingtimes (see Table 1 in the mDHFR PCA description), and undertook aselection/enrichment of the novel zippers relative to GCN4, as follows.The designed zipper libraries, expressed as N-terminal fusions to theDHFR F[1,2] or F[3:I114A], were cotransformed, clones were picked,propagated and mixed in selective liquid culture, and the mix was addedin a 1:1 000 000 ratio to clone Z-F[1,2]+Z-F[3:I114 A] (original GCN4leucine zippers). The mixture was propagated in selective liquid cultureover multiple passages. Restriction analysis shows that within 4passages, the population of GCN4-expressing bacteria is diminishingrelative to the novel zipper sequences (data not shown), indicating thatsome of the designed zipper-containing clones are propagated at a higherrate than those containing GCN4. Bacteria from later passages wereplated on selective medium, and individual clones sequenced to revealthe identity of the most successful designed zipper pairs (data notshown).2) Application of PCA to enzyme function and design PCA Development:Adenosine deaminase (ADA) meets all of the criteria for a PCA listedabove. ADA is a small (˜40 kD), and easily purified monomeric zincmetallo-enzyme and the structure of murine ADA has been resolved.Several in vitro ADA activity assays have been developed, involving UVspectrophotometry and stopped-flow fluorimetry. E. coli ADA catalyzesthe irreversible conversion of cytotoxic adenine nucleosides tonon-toxic inosines.

Eukaryotic or prokaryotic cells propagated in the presence of cytotoxicconcentrations of adenosine or adenosine analogs require ADA to detoxifythese compounds. This is the basis of a dominant-selection strategy usedto select for cells expressing a specific gene in mammalian cells. TheADA gene has also been expressed in SF3834 E. coli cells which lack agene coding for endogenous ADA. When the gene coding for ADA isintroduced into ADA—bacterial DNA, those cells that express ADA are ableto survive high concentrations of added adenosine; those that do not,die. This forms the basis of an in vivo ADA activity assay.

We chose ADA, principally because it can be used as a dominant selectivemarker in mammalian and bacterial cells where the gene has been knockedout. The reason we choose dominant selective genes is because inscreening for novel protein-protein interactions, particularly testingfor interactions of a known protein against a library of millions ofindependent clones, selection serves to filter for cells that may show apositive response for reasons having nothing to do with a specificprotein-protein interaction. We will use three test systems ofinteracting proteins including leucine zipper-forming sequences, theproteins raf and p21 and the induced oligomerization system, FK506binding protein (FKBP) and mTOR that interact through the macrocyclicimmuno-suppressant compound rapamycin. For all of these systems, we willconstruct E. coli and mammalian transient transfection plasmids andsubclone the test proteins as fusions to ADA complementary fragments.The primary assay will be survival of SF3834 E. coli cells that havebeen transformed with the complementary ADA fragments fused to the testoligomerization proteins in the presence of toxic concentrations ofadenosine. We will then purify fusion proteins from colonies of andperform in vitro assays of ADA activity as described below. The utilityof the ADA PCA as a method to identify novel proteins that interact witha test bait will be performed in mammalian COS-7 and HEK-293T cellstransiently transfected with FKBP fused to one of the ADA fragments andthe other fragment fused to a cDNA library from normal human spleencontaining 10⁶ independent clones. As with the E. coli assay, cells thatsurvive in a medium containing toxic concentrations of ADA is collectedand isolated plasmids will be tested to identify the gene for theinteracting protein by PCR amplification and chainpropagation-termination techniques.

Structural motifs required for protein function: Determination of thestructural elements required for the enzymatic function of ADA areinvestigated through alteration of the structures of the enzymefragments. At first, ADA is cut into two separate domains—oneresponsible for substrate binding (residues 1-210) and one responsiblefor catalysis (residues 211-352). These separate pieces will be attachedto known assembly domains, such as leucine zippers (see example 1above). Reassembly will restore activity which will be assessed throughdetailed in vitro kinetic analysis of the binding and catalyticproperties of the re-assembled enzyme, using UV spectrophotometry andstopped-flow fluorimetry to observe the enzymatic reactions. This systemwill provide another handle on the manipulation of enzyme activity thatwill afford a powerful tool for enzymatic mechanism study. For example,the difference in the kinetic behaviour of the reassembled enzyme onmixing with the substrate, compared to enzyme reassembled in presence ofsubstrate (where substrate may already be bound by binding domain) willallow sophisticated level of study of importance of binding energy tocatalysis. Subsequent point mutations to the functional or assemblydomains of the proteins will then allow a very subtle perturbation anddetailed quantification of the relationship of binding energy tocatalysis. This precise control over the structure and assembly ofseparate functional domains of the enzyme will permit very sophisticatedenzymatic structure function studies, the definition of structuralmotifs and an understanding of their role in catalysis.Novel protein catalyst design: The detailed knowledge of the enzymemechanism gained through determination of the structural requirementsfor catalysis will then be exploited through the combination of thesefunctional “building blocks” with the functional motifs responsible forsubstrate binding and catalysis in other enzymes, allowing thegeneration of novel protein catalysts. For example, the catalytic motiffrom ADA is modified to a cytidine-binding motif, creating a novelenzyme with potentially useful catalytic properties. The activity ofthese novel enzymes can easily be assessed through in vivo assayssimilar to that of the PCA system, or through in vitro activity assays.Furthermore, the detailed mechanistic investigation of the resultingenzymes possible with this system will permit the rational design ofeach subsequent generation of catalysts.

Example 8 Examples of Applications the PCA Strategy to Detect MolecularInteractions in Whole Organisms

It is a logical extension of the descriptions of PCA applications aboveto the utility of these techniques in whole model organisms such asdrosophila, nematodes, zebra fish and puffer fish, as examples. The soledifferences with other listed examples is that vectors used would needto be different (for example retroviral vectors) and that any substratesneeded by the PCA would need to be bioavailable, or detection would needto be performed in situ.

Example 9 Examples of Applications of the PCA Strategy to Gene Therapy

Another important embodiment of the invention is to provide a means andmethod for gene therapy of mammalian disease. Of particular interest isthe use of PCA therapeutic for treatment of cancer. In one embodiment ofsaid PCA gene therapy, a PCA is developed employing fragments (modularprotein units) derived from a protein toxin for example: Pseudomonasexotoxin, Diptheria toxin and the plant toxin gelonin, or other likemolecules. For therapy of breast cancer for example, first a mammalian,retroviral, adenoviral, or eukaryotic artificial chromosomal (EAC's)genetic construct is prepared that introduces one fragment of theselected toxin under the control of the promoter for expression of theerbB2 oncogene. Its is well known that the erbB2 oncogene isoverexpressed in breast cancer and adenocarcinoma cells (D. J. Slamonet. al., Science, 1989, 244, 707). The HER2/neu (c-erbB-2)proto-oncogene encodes a sub-class 1 185-kDa transmembrane proteintyrosine kinase growth factor receptor, p185^(HER2). Also, the humanerbB2 oncogene is located on chromosome 17, region q21 and comprises4,480 base pairs and p185^(HER2) serves as a receptor for a 30-kDaglycoprotein growth factor secreted by human breast cancer cell lines(R. Lupu et. Al., Science, 1990, 249, 1152).

The transgene is introduced ‘in vivo’ or ‘ex-vivo’ into target cellsemploying methods known by those skilled in the art e.g. homologousrecombination to insert transgene into locus of interest via retroviral,adenoviral or EAC's. A second genetic construct comprising a fusion genecontaining a target DNA that encodes an interacting protein thatinteracts with erbB2 oncogene discovered by the PCA process described inthis invention and the “second” fragment of the toxin molecule. Thisconstruct is delivered to the patient by methods known in the art forexample as shown in U.S. Pat. Nos. 5,399,346 and 5,585,237 whose entirecontents are incorporated by reference herein. Transgene expression ofthe erbB2 oncogene-toxin fragment described will now be under thecontrol of the constitutive oncogene promoter. Proliferating tumor cellswill thus produce one piece of the toxin attached as a fusion to theerbB2 oncogene. In the presence of the second genetic constructexpressing the PCA discovered interacting erbB2 oncogene “interactingprotein-toxin fragment” construct then: erbB2 oncogene-toxin fragmentA:interacting protein-toxin fragment B will be created and induce death oftarget tumor cells through creation of an active toxin through ProteinFragment Complementation and thus provide an efficacious and efficienttherapy of said disease.

This can be extended to other diseases and other toxins employingtechniques described and embodied in this invention.

Example 10 Examples of Applications the PCA Strategy to Detect MolecularInteractions In Vitro

Any of the PCA strategies described above could be adapted to in vitrodetection. Unlike the in vivo PCAs however, detection would be performedwith purified PCA fragment-fusion proteins. Such uses of PCA have thepotential for use in diagnostic kits. For example the test DHFR assaydescribed above where the interacting domains are FKBP12 and TOR couldbe used as a diagnostic test for rapamycin concentrations for use inmonitoring dosage in patients treated with this drug.As shown above, the instant invention provides:1) Allow for the detection of protein-protein interactions in vivo or invitro.2) Allow for the detection of protein-protein interactions inappropriate contexts, such as within a specific organism, cell type,cellular compartment, or organelle.3) Allow for the detection of induced versus constitutiveprotein-protein interactions (such as by a cell growth or inhibitoryfactor).4) To be able to distinguish specific-versus non-specificprotein-protein interactions by controlling the sensitivity of theassay.5) Allow for the detection of the kinetics of protein assembly in cells.6) Allow for screening of cDNA libraries for protein-proteininteractions.

Further aspects of the invention can be demonstrated by identifyingnovel interactions with the enzyme p70S6k, to determine its' regulationand how separate signaling cascades converge on this enzyme.

The PCA method is particularly useful for detection of the kinetics ofprotein assembly in cells. The kinetics of protein assembly can bedetermined using fluorescent protein systems.

In a further embodiment of the invention, PCA can be used for drugscreening. The techniques of PCA are used to screen for drugs that blockspecific biochemical pathways in cells allowing for a carefully targetedand controlled method for identifying products that have usefulpharmacological properties.

Although the present invention has been described herein above by way ofpreferred embodiments thereof, it can be modified, without departingfrom the spirit and nature of the subject invention as defined in theappended claims.

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1. Molecular fragment complementation assays for the detection ofmolecular interactions comprising a reassembly of separate fragments ofa molecule, wherein reassembly of said fragments is operated by theinteraction of molecular domains fused to each fragment of saidmolecules, and wherein reassembly of the fragments is independent ofother molecular processes. 2-58. (canceled)
 59. A composition comprisinga complementary fragment of a first protein molecule which exhibits adetectable activity when associated, fused to a separate proteinmolecule.